Use of microvesicles in diagnosis and prognosis of medical diseases and conditions

ABSTRACT

The presently disclosed subject matter is directed to methods of aiding diagnosis, prognosis, monitoring and evaluation of a disease or other medical condition in a subject by detecting a biomarker in microvesicles isolated from a biological sample from the subject.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation application of co-pending U.S. patent application Ser. No. 15/374,477 filed Dec. 9, 2016, which is a continuation application of co-pending U.S. patent application Ser. No. 14/924,245 filed Oct. 27, 2015, which is a continuation of U.S. patent application Ser. No. 13/939,242 filed Jul. 11, 2013, now abandoned, which is a continuation of U.S. patent application Ser. No. 13/688,273 filed Nov. 29, 2012, now abandoned, which is a continuation of U.S. patent application Ser. No. 12/865,681 filed Nov. 8, 2010, now abandoned, which is a 35 U.S.C. §371 National Phase Entry Application of International Application No. PCT/US2009/032881 filed Feb. 2, 2009, which designates the U.S., and which claims benefit under 35 U.S.C. §119(e) of U.S. Provisional No. 61/025,536 filed Feb. 1, 2008 and U.S. Provisional No. 61/100,293 filed Sep. 26, 2008, the contents of each of which are incorporated herein by reference in their entireties.

GOVERNMENTAL SUPPORT

This invention was made with Government support under grants NCI CA86355 and NCI CA69246 awarded by the National Cancer Institute. The Government has certain rights in the invention.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted in ASCII format via EFS-Web and is hereby incorporated by reference in its entirety. Said ASCII copy, created on May 5, 2017, is named SL_030258-084114-C7.txt and is 12,814 bytes in size.

FIELD OF THE INVENTION

The present invention relates to the fields of medical diagnosis, patient monitoring, treatment efficacy evaluation, nucleic acid and protein delivery, and blood transfusion.

BACKGROUND OF THE INVENTION

Glioblastomas are highly malignant brain tumors with a poor prognosis despite intensive research and clinical efforts (Louis et al., 2007). The invasive nature of this tumor makes complete surgical resection impossible and the median survival time is only about 15 months (Stupp et al., 2005). Glioblastoma cells as well as many other tumor cells have a remarkable ability to mold their stromal environment to their own advantage. Tumor cells directly alter surrounding normal cells to facilitate tumor cell growth, invasion, chemoresistance, immune-evasion and metastasis (Mazzocca et al., 2005; Muerkoster et al., 2004; Singer et al., 2007). The tumor cells also hijack the normal vasculature and stimulate rapid formation of new blood vessels to supply the tumor with nutrition (Carmeliet and Jain, 2000). Although the immune system can initially suppress tumor growth, it is often progressively blunted by tumor activation of immunosuppressive pathways (Gabrilovich, 2007).

Small microvesicles shed by cells are known as exosomes (Thery et al., 2002). Exosomes are reported as having a diameter of approximately 30-100 nm and are shed from many different cell types under both normal and pathological conditions (Thery et al., 2002). These microvesicles were first described as a mechanism to discard transferrin-receptors from the cell surface of maturing reticulocytes (Pan and Johnstone, 1983). Exosomes are formed through inward budding of endosomal membranes giving rise to intracellular multivesicular bodies (MVB) that later fuse with the plasma membrane, releasing the exosomes to the exterior (Thery et al., 2002). However, there is now evidence for a more direct release of exosomes. Certain cells, such as Jurkat T-cells, are said to shed exosomes directly by outward budding of the plasma membrane (Booth et al., 2006). All membrane vesicles shed by cells are referred to herein collectively as microvesicles.

Microvesicles in Drosophila melanogaster, so called argosomes, are said to contain morphogens such as Wingless protein and to move over large distances through the imaginal disc epithelium in developing Drosophila melanogaster embryos (Greco et al., 2001). Microvesicles found in semen, known as prostasomes, are stated to have a wide range of functions including the promotion of sperm motility, the stabilization of the acrosome reaction, the facilitation of immunosuppression and the inhibition of angiogenesis (Delves et al., 2007). On the other hand, prostasomes released by malignant prostate cells are said to promote angiogenesis. Microvesicles are said to transfer proteins (Mack et al., 2000) and recent studies state that microvesicles isolated from different cell lines can also contain messenger RNA (mRNA) and microRNA (miRNA) and can transfer mRNA to other cell types (Baj-Krzyworzeka et al., 2006; Valadi et al., 2007).

Microvesicles derived from B-cells and dendritic cells are stated to have potent immuno-stimulatory and antitumor effects in vivo and have been used as antitumor vaccines (Chaput et al., 2005). Dendritic cell-derived microvesicles are stated to contain the co-stimulatory proteins necessary for T-cell activation, whereas most tumor cell-derived microvesicles do not (Wieckowski and Whiteside, 2006). Microvesicles isolated from tumor cells may act to suppress the immune response and accelerate tumor growth (Clayton et al., 2007; Liu et al., 2006a). Breast cancer microvesicles may stimulate angiogenesis, and platelet-derived microvesicles may promote tumor progression and metastasis of lung cancer cells (Janowska-Wieczorek et al., 2005; Millimaggi et al., 2007).

Cancers arise through accumulation of genetic alterations that promote unrestricted cell growth. It has been stated that each tumor harbors, on average, around 50-80 mutations that are absent in non-tumor cells (Jones et al., 2008; Parsons et al., 2008; Wood et al., 2007). Current techniques to detect these mutation profiles include the analysis of biopsy samples and the non-invasive analysis of mutant tumor DNA fragments circulating in bodily fluids such as blood (Diehl et al., 2008). The former method is invasive, complicated and possibly harmful to subjects. The latter method inherently lacks sensitivity due to the extremely low copy number of mutant cancer DNA in bodily fluid (Gormally et al., 2007). Therefore, one challenge facing cancer diagnosis is to develop a diagnostic method that can detect tumor cells at different stages non-invasively, yet with high sensitivity and specificity. It has also been stated that gene expression profiles (encoding mRNA or microRNA) can distinguish cancerous and non-cancerous tissue (Jones et al., 2008; Parsons et al., 2008; Schetter et al., 2008). However, current diagnostic techniques to detect gene expression profiles require intrusive biopsy of tissues. Some biopsy procedures cause high risk and are potentially harmful. Moreover, in a biopsy procedure, tissue samples are taken from a limited area and may give false positives or false negatives, especially in tumors which are heterogeneous and/or dispersed within normal tissue. Therefore, a non-intrusive and sensitive diagnostic method for detecting biomarkers would be highly desirable.

SUMMARY OF THE INVENTION

In general, the invention is a novel method for detecting in a subject the presence or absence of a variety of biomarkers contained in microvesicles, thereby aiding the diagnosis, monitoring and evaluation of diseases, other medical conditions, and treatment efficacy associated with microvesicle biomarkers.

One aspect of the invention are methods for aiding in the diagnosis or monitoring of a disease or other medical condition in a subject, comprising the steps of: a) isolating a microvesicle fraction from a biological sample from the subject; and b) detecting the presence or absence of a biomarker within the microvesicle fraction, wherein the biomarker is associated with the disease or other medical condition. The methods may further comprise the step or steps of comparing the result of the detection step to a control (e.g., comparing the amount of one or more biomarkers detected in the sample to one or more control levels), wherein the subject is diagnosed as having the disease or other medical condition (e.g., cancer) if there is a measurable difference in the result of the detection step as compared to a control.

Another aspect of the invention is a method for aiding in the evaluation of treatment efficacy in a subject, comprising the steps of: a) isolating a microvesicle fraction from a biological sample from the subject; and b) detecting the presence or absence of a biomarker within the microvesicle fraction, wherein the biomarker is associated with the treatment efficacy for a disease or other medical condition. The method may further comprise the step of providing a series of a biological samples over a period of time from the subject. Additionally, the method may further comprise the step or steps of determining any measurable change in the results of the detection step (e.g., the amount of one or more detected biomarkers) in each of the biological samples from the series to thereby evaluate treatment efficacy for the disease or other medical condition.

In certain preferred embodiments of the foregoing aspects of the invention, the biological sample from the subject is a sample of bodily fluid. Particularly preferred body fluids are blood and urine.

In certain preferred embodiments of the foregoing aspects of the invention, the methods further comprise the isolation of a selective microvesicle fraction derived from cells of a specific type (e.g., cancer or tumor cells). Additionally, the selective microvesicle fraction may consist essentially of urinary microvesicles.

In certain embodiments of the foregoing aspects of the invention, the biomarker associated with a disease or other medical condition is i) a species of nucleic acid; ii) a level of expression of one or more nucleic acids; iii) a nucleic acid variant; or iv) a combination of any of the foregoing. Preferred embodiments of such biomarkers include messenger RNA, microRNA, DNA, single stranded DNA, complementary DNA and noncoding DNA.

In certain embodiments of the foregoing aspects of the invention, the disease or other medical condition is a neoplastic disease or condition (e.g., glioblastoma, pancreatic cancer, breast cancer, melanoma and colorectal cancer), a metabolic disease or condition (e.g., diabetes, inflammation, perinatal conditions or a disease or condition associated with iron metabolism), a post transplantation condition, or a fetal condition.

Another aspect of the invention is a method for aiding in the diagnosis or monitoring of a disease or other medical condition in a subject, comprising the steps of a) obtaining a biological sample from the subject; and b) determining the concentration of microvesicles within the biological sample.

Yet another aspect of this invention is a method for delivering a nucleic acid or protein to a target cell in an individual comprising the steps of administering microvesicles which contain the nucleic acid or protein, or one or more cells that produce such microvesicles, to the individual such that the microvesicles enter the target cell of the individual. In a preferred embodiment of this aspect of the invention, microvesicles are delivered to brain cells.

A further aspect of this invention is a method for performing bodily fluid transfusion (e.g., blood, serum or plasma), comprising the steps of obtaining a fraction of donor body fluid free of all or substantially all microvesicles, or free of all or substantially all microvesicles from a particular cell type (e.g., tumor cells), and introducing the microvesicle-free fraction to a patient. A related aspect of this invention is a composition of matter comprising a sample of body fluid (e.g., blood, serum or plasma) free of all or substantially all microvesicles, or free of all or substantially all microvesicles from a particular cell type.

Another aspect of this invention is a method for performing bodily fluid transfusion (e.g., blood, serum or plasma), comprising the steps of obtaining a microvesicle-enriched fraction of donor body fluid and introducing the microvesicle-enriched fraction to a patient. In a preferred embodiment, the fraction is enriched with microvesicles derived from a particular cell type. A related aspect of this invention is a composition of matter comprising a sample of bodily fluid (e.g., blood, serum or plasma) enriched with microvesicles.

A further aspect of this invention is a method for aiding in the identification of new biomarkers associated with a disease or other medical condition, comprising the steps of obtaining a biological sample from a subject; isolating a microvesicle fraction from the sample; and detecting within the microvesicle fraction species of nucleic acid; their respective expression levels or concentrations; nucleic acid variants; or combinations thereof.

Various aspects and embodiments of the invention will now be described in detail. It will be appreciated that modification of the details may be made without departing from the scope of the invention. Further, unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular.

All patents, patent applications, and publications identified are expressly incorporated herein by reference for the purpose of describing and disclosing, for example, the methodologies described in such publications that might be used in connection with the present invention. These publications are provided solely for their disclosure prior to the filing date of the present application. Nothing in this regard should be construed as an admission that the inventors are not entitled to antedate such disclosure by virtue of prior invention or for any other reason. All statements as to the date or representations as to the contents of these documents are based on the information available to the applicants and do not constitute any admission as to the correctness of the dates or contents of these documents.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1F. Glioblastoma cells produce microvesicles containing RNA. FIG. 1 (a) Scanning electron microscopy image of a primary glioblastoma cell (bar=10 μm). FIG. 1 (b) Higher magnification showing the microvesicles on the cell surface. The vesicles vary in size with diameters between around 50 nm and around 500 nm (bar=1 μm). FIG. 1 (c) Graph showing the amount of total RNA extracted from microvesicles that were either treated or not treated with RNase A. The amounts are indicated as the absorption (Abs, y-axis) of 260 nm wavelength (x-axis). The experiments were repeated 5 times and a representative graph is shown. FIG. 1 (d) Bioanalyzer data showing the size distribution of total RNA extracted from primary glioblastoma cells and FIG. 1 (e) Bioanalyzer data showing the size distribution of total RNA extracted from microvesicles isolated from primary glioblastoma cells. The 25 nt peak represents an internal standard. The two prominent peaks in FIG. 1 (d) (arrows) represent 18S (left arrow) and 28S (right arrow) ribosomal RNA. The ribosomal peaks are absent from RNA extracted from microvesicles FIG. 1 (e). FIG. 1 (f) Transmission electron microscopy image of microvesicles secreted by primary glioblastoma cells (bar=100 nm).

FIGS. 2A-2D. Analysis of microvesicle RNA. FIG. 2 (a) and FIG. 2 (b) are scatter plots of mRNA levels in microvesicles and mRNA levels in donor glioblastoma cells from two different experiments. Linear regressions show that mRNA levels in donor cells versus microvesicles were not well correlated. FIG. 2 (c) and FIG. 2 (d) are mRNA levels in two different donor cells or two different microvesicle preparations. In contrast to FIG. 2 (a) and FIG. 2 (b), linear regressions show that mRNA levels between donor cells FIG. 2 (c) or between microvesicles FIG. 2 (d) were closely correlated.

FIGS. 3A-3I. Analysis of microvesicle DNA.

FIG. 3 a) GAPDH gene amplification with DNA templates from exosomes treated with DNase prior to nucleic acid extraction. The lanes are identified as follows:

1. 100 bp MW ladder

2. Negative control

3. Genomic DNA control from GBM 20/3 cells

4. DNA from normal serum exosomes (tumor cell-free control)

5. Exosome DNA from normal human fibroblasts (NHF19)

6. Exosome DNA from primary medulloblastoma cells (D425)

FIG. 3 b) GAPDH gene amplification with DNA templates from exosomes without prior DNase treatment. The lanes are identified as follows:

1. 100 bp MW ladder

2. DNA from primary melanoma cell 0105

3. Exosome DNA from melanoma 0105

4. Negative Control

5. cDNA from primary GBM 20/3 (positive control)

FIG. 3 c) Human Endogenous Retrovirus K gene amplification. The lanes are identified as follows:

1. 100 bp MW ladder

2. Exosome DNA from medulloblastoma D425 a

3. Exosome DNA from medulloblastoma D425 b

4. Exosome DNA from normal human fibroblasts (NHF19)

5. Exosome DNA from normal human serum

6. Genomic DNA from GBM 20/3.

7. Negative Control

FIG. 3 d) Tenascin C gene amplification. The lanes are listed identified follows:

1. 100 bp MW ladder

2. Exosomes from normal human fibroblasts (NHF19)

3. Exosomes from serum (tumor cell free individual A)

4. Exosomes from serum (tumor cell free individual B)

5. Exosomes from primary medulloblastoma cell D425

FIG. 3 e) Transposable Line 1 element amplification. The lanes are identified as follows:

1. 100 bp MW ladder.

2. Exosome DNA from normal human serum.

3. Exosome DNA from normal human fibroblasts

4. Exosome DNA from medulloblastoma D425 a

5. Exosome DNA from medulloblastoma D425 b

FIG. 3 f) DNA is present in exosomes from D425 medulloblastoma cell. The lanes are identified as follows:

1. 100 bp marker

2. D425 no DNase

3. D425 with DNase

4. Ikb marker

FIG. 3 g) Single stranded nucleic acid analysis using a RNA pico chip. Upper panel: purified DNA was not treated with DNase; lower panel: purified DNA was treated with DNase. The arrow in the upper panel refers to the detected nucleic acids. The peak at 25 nt is an internal standard.

FIG. 3 h) Analysis of nucleic acids contained in exosomes from primary medulloblastoma D425. Upper panel: single stranded nucleic acids detected by a RNA pico chip. Lower panel: double stranded nucleic acids detected by a DNA 1000 chip. The arrow in the upper panel refers to the detected nucleic acids. The two peaks (15 and 1500 bp) are internal standards.

FIG. 3 i) Analysis of exosome DNA from different origins using a RNA pico chip. Upper panel: DNA was extracted from exosomes from glioblastoma cells. Lower panel: DNA was extracted from exosomes from normal human fibroblasts.

FIGS. 4A-4C. Extracellular RNA extraction from serum is more efficient when a serum exosome isolation step is included. FIG. 4 a) Exosome RNA from serum. FIG. 4 b) Direct whole serum extraction. FIG. 4 c) Empty well. Arrows refer to the detected RNA in the samples.

FIG. 5. Comparison of gene expression levels between microvesicles and cells of origin. 3426 genes were found to be more than 5-fold differentially distributed in the microvesicles as compared to the cells from which they were derived (p-value <0.01).

FIGS. 6A-6B. Ontological analysis of microvesicular RNAs. FIG. 6 (a) Pie chart displays the biological process ontology of the 500 most abundant mRNA species in the microvesicles. FIG. 6 (b) Graph showing the intensity of microvesicle RNAs belonging to ontologies related to tumor growth. The x-axis represents the number of mRNA transcripts present in the ontology. The median intensity levels on the arrays were 182.

FIG. 7. Clustering diagram of mRNA levels. Microarray data on the mRNA expression profiles in cell lines and exosomes isolated from the culture media of these cell lines were analyzed and clusters of expression profiles were generated. The labels of the RNA species are as follows:

20/3C-1: Glioblastoma 20/3 Cell RNA, array replicate 1

20/3C-2: Glioblastoma 20/3 Cell RNA, array replicate 2

11/5C: Glioblastoma 11/5 Cell RNA

0105C: Melanoma 0105 Cell RNA

0664C: Melanoma 0664 Cell RNA

0664 E-1: Melanoma 0664 exosome RNA, array replicate 1

0664 E-2: Melanoma 0664 exosome RNA, array replicate 2

0105E: Melanoma 0105 Exosome RNA

20/3E: Glioblastoma 20/3 Exosome RNA

11/5E-1: Glioblastoma 11/5 Exosomes, array replicate 1

11/5E-2: Glioblastoma 11/5 Exosomes, array replicate 2

GBM: glioblastoma. The scale refers to the distance between clusters.

FIG. 8. Microvesicles from serum contain microRNAs. Levels of mature miRNAs extracted from microvesicles and from glioblastoma cells from two different patients (GBM1 and GBM2) were analysed using quantitative miRNA RT-PCR. The cycle threshold (Ct) value is presented as the mean±SEM (n=4).

FIG. 9. Clustering diagram of microRNA levels. Microarray data on the microRNA expression profiles in cell lines and exosomes isolated from the culture media of these cell lines were analyzed and clusters of expression profiles were generated. The labels of the RNA species are as follows:

0664C-1: Melanoma 0664 Cell RNA, array replicate 1

0664C-2: Melanoma 0664 Cell RNA, array replicate 2

0105C-1: Melanoma 0105 Cell RNA, array replicate 1

0105C-2: Melanoma 0105 Cell RNA, array replicate 2

20/3C-1: Glioblastoma 20/3 Cell RNA, array replicate 1

20/3C-2: Glioblastoma 20/3 Cell RNA, array replicate 2

11/5C-1: Glioblastoma 11/5 Cell RNA, array replicate 1

11/5C-2: Glioblastoma 11/5 Cell RNA, array replicate 2

11/5E-1: Glioblastoma 11/5 Exosomes, array replicate 1

11/5E-2: Glioblastoma 11/5 Exosomes, array replicate 2

20/3E-1: Glioblastoma 20/3 Exosome RNA, array replicate 1

20/3E-2: Glioblastoma 20/3 Exosome RNA, array replicate 2

0664 E: Melanoma 0664 exosome RNA

0105E-1: Melanoma 0105 Exosome RNA, array replicate 1

0105E-2: Melanoma 0105 Exosome RNA, array replicate 2

GBM: Glioblastoma. The scale refers to the distance between clusters.

FIG. 10. The expression level of microRNA-21 in serum microvesicles is associated with glioma. Shown is a bar graph, normal control serum on the left, glioma serum on the right. Quantitative RT-PCR was used to measure the levels of microRNA-21 (miR-21) in exosomes from serum of glioblastoma patients as well as normal patient controls. Glioblastoma serum showed a 5.4 reduction of the Ct-value, corresponding to an approximately 40 (2ΔCt)-fold increase of miR21. The miR21 levels were normalized to GAPDH in each sample (n=3).

FIG. 11. Nested RT-PCR was used to detect EGFRvIII mRNA in tumor samples and corresponding serum exosomes. The wild type EGFR PCR product appears as a band at 1153 bp and the EGFRvIII PCR product appears as a band at 352 bp. RT PCR of GAPDH mRNA was included as a positive control (226 bp). Samples considered as positive for EGFRvIII are indicated with an asterisk. Patients 11, 12 and 14 showed only a weak amplification of EGFRvIII in the tumor sample, but it was evident when more samples were loaded.

FIG. 12. Nested RT PCR of EGFRvIII was performed on microvesicles from 52 normal control serums. EGFRvIII (352 bp) was never found in the normal control serums. PCR of GAPDH (226 bp) was included as a control.

FIGS. 13A-13D. Hepcidin mRNA can be detected within exosomes from human serum. FIG. 13 A) Pseudo-gel generated by an Agilent Bioanalyzer. FIG. 13 B) Raw plot generated by an Agilent Bioanalyser for the positive control (Sample 1). FIG. 13 C) Raw plot generated by an Agilent Bioanalyser for the negative control (Sample 2). FIG. 13 D) Raw plot generated by an Agilent Bioanalyser for the exosomes (Sample 3).

FIGS. 14A-14H. Urinary exosome isolation and nucleic acid identification within urinary exosomes. FIG. 14 (a) Electron microscopy image of a multivesicular body (MVB) containing many small “exosomes” in a kidney tubule cell. FIG. 14 (b) Electron microscopy image of isolated urinary exosomes. FIG. 14 (c) Analysis of RNA transcripts contained within urinary exosomes by an Agilent Bioanalyzer. A broad range of RNA species were identified but both 18S and 28S ribosomal RNAs were absent. FIG. 14 (d) Identification of various RNA transcripts in urinary exosomes by PCR. The transcripts thus identified were: Aquaporin 1 (AQP1); Aquaporin 2 (AQP2); Cubulin (CUBN); Megalin (LRP2); Arginine Vasopressin Receptor 2 (AVPR2); Sodium/Hydrogen Exchanger 3 (SLC9A3); V-ATPase B1 subunit (ATP6V1B1); Nephrin (NPHS1); Podocin (NPHS2); and Chloride Channel 3 (CLCN3). From top to bottom, the five bands in the molecular weight (MW) lane correspond to 1000, 850, 650, 500, 400, 300 base pair fragments. FIG. 14 (e) Bioanalyzer diagrams of exosomal nucleic acids from urine samples. The numbers refer to the numbering of human individuals. FIG. 14 (f) Pseudogels depicting PCR products generated with different primer pairs using the nucleic acid extracts described in FIG. 14 (e). House refers to actin gene and the actin primers were from Ambion (TX, USA). The +ve control refers to PCRs using human kidney cDNA from Ambion (TX, USA) as templates and the −ve control refers to PCRs without nucleic acid templates. FIG. 14 (g) Pseudo-gel picture showing positive identification of actin gene cDNA via PCR with and without the DNase treatment of exosomes prior to nucleic acid extraction. FIG. 14 (h) Bioanalyzer diagrams showing the amount of nucleic acids isolated from human urinary exosomes.

FIGS. 15A-15C. Analysis of prostate cancer biomarkers in urinary exosomes. FIG. 15 (a) Gel pictures showing PCR products of the TMPRSS2-ERG gene and digested fragments of the PCR products. P1 and P2 refer to urine samples from patient 1 and patient 2, respectively. For each sample, the undigested product is in the left lane and the digested product is in the right lane. MWM indicates lanes with MW markers. The sizes of the bands (both undigested and digested) are indicated on the right of the panel. FIG. 15 (b) Gel pictures showing PCR products of the PCA3 gene and digested fragments of the PCR products. P1, P2, P3 and P4 refer to urine samples from patient 1, patient 2, patient 3 and patient 4, respectively. For each sample, the undigested product is in the left lane and the digested product is in the right lane. MWM indicates lanes with MW markers. The sizes of the bands (both undigested and digested) are indicated on the right of the panel. FIG. 15 (c) A summary of the information of the patients and the data presented in FIG. 15 (a) and FIG. 15 (b). TMERG refers to the TMPRSS2-ERG fusion gene.

FIGS. 16A-16D. BRAF mRNA is contained within microvesicles shed by melanoma cells. FIG. 16 (a) An electrophoresis gel picture showing RT-PCR products of BRAF gene amplification. FIG. 16 (b) An electrophoresis gel picture showing RT-PCR products of GAPDH gene amplification. The lanes and their corresponding samples are as follows: Lane #1-100 bp Molecular Weight marker; Lane #2—YUMEL-01-06 exo; Lane #3—YUMEL-01-06 cell; Lane #4 YUMEL-06-64 exo; Lane #5. YUMEL-06-64 cell; Lane #6. M34 exo; Lane #7—M34 cell; Lane #8—Fibroblast cell; Lane #9—Negative control. The reference term “exo” means that the RNA was extracted from exosomes in the culture media. The reference term “cell” means that the RNA was extracted from the cultured cells. The numbers following YUMEL refers to the identification of a specific batch of YUMEL cell line. FIG. 16 (c) Sequencing results of PCR products from YUMEL-01-06 exo. The results from YUMEL-01-06 cell, YUMEL-06-64 exo and YUMEL-06-64 cell are the same as those from YUMEL-01-06 exo. FIG. 16 (d) Sequencing results of PCR products from M34 exo. The results from M34 cell are the same as those from M34 exo.

FIGS. 17A-17C. Glioblastoma microvesicles can deliver functional RNA to HBMVECs. FIG. 17 (a) Purified microvesicles were labelled with membrane dye PKH67 (green) and added to HBMVECs. The microvesicles were internalised into endosome-like structures within an hour. FIG. 17 (b) Microvesicles were isolated from glioblastoma cells stably expressing Gluc. RNA extraction and RT-PCR of Gluc and GAPDH mRNAs showed that both were incorporated into microvesicles. FIG. 17 (c) Microvesicles were then added to HBMVECs and incubated for 24 hours. The Gluc activity was measured in the medium at 0, 15 and 24 hours after microvesicle addition and normalized to Gluc activity in microvesicles. The results are presented as the mean±SEM (n=4).

FIGS. 18A-18C. Glioblastoma microvesicles stimulate angiogenesis in vitro and contain angiogenic proteins. FIG. 18 (a) HBMVECs were cultured on Matrigel™ in basal medium (EBM) alone, or supplemented with GBM microvesicles (EBM+MV) or angiogenic factors (EGM). Tubule formation was measured after 16 hours as average tubule length ±SEM compared to cells grown in EBM (n=6). FIG. 18 (b) Total protein from primary glioblastoma cells and microvesicles (MV) from these cells (1 mg each) were analysed on a human angiogenesis antibody array. FIG. 18 (c) The arrays were scanned and the intensities analysed with the Image J software (n=4).

FIGS. 19A-19C. Microvesicles isolated from primary glioblastoma cells promote proliferation of the U87 glioblastoma cell line. 100,000 U87 cells were seeded in wells of a 24 well plate and allowed to grow for three days in FIG. 19 (a) normal growth medium (DMEM-5% FBS) or FIG. 19 (b) normal growth medium supplemented with 125 microvesicles. FIG. 19 (c) After three days, the non-supplemented cells had expanded to 480,000 cells, whereas the microvesicle-supplemented cells had expanded to 810,000 cells. NC refers to cells grown in normal control medium and MV refers to cells grown in medium supplemented with microvesicles. The result is presented as the mean±SEM (n=6).

DETAILED DESCRIPTION OF THE INVENTION

Microvesicles are shed by eukaryotic cells, or budded off of the plasma membrane, to the exterior of the cell. These membrane vesicles are heterogeneous in size with diameters ranging from about 10 nm to about 5000 nm. The small microvesicles (approximately 10 to 1000 nm, and more often 30 to 200 nm in diameter) that are released by exocytosis of intracellular multivesicular bodies are referred to in the art as “exosomes”. The methods and compositions described herein are equally applicable to microvesicles of all sizes; preferably 30 to 800 nm; and more preferably 30 to 200 nm.

In some of the literature, the term “exosome” also refers to protein complexes containing exoribonucleases which are involved in mRNA degradation and the processing of small nucleolar RNAs (snoRNAs), small nuclear RNAs (snRNAs) and ribosomal RNAs (rRNA) (Liu et al., 2006b; van Dijk et al., 2007). Such protein complexes do not have membranes and are not “microvesicles” or “exosomes” as those terms are used here in.

Exosomes as Diagnostic and/or Prognostic Tools

Certain aspects of the present invention are based on the surprising finding that glioblastoma derived microvesicles can be isolated from the serum of glioblastoma patients. This is the first discovery of microvesicles derived from cells in the brain, present in a bodily fluid of a subject. Prior to this discovery it was not known whether glioblastoma cells produced microvesicles or whether such microvesicles could cross the blood brain barrier into the rest of the body. These microvesicles were found to contain mutant mRNA associated with tumor cells. The microvesicles also contained microRNAs (miRNAs) which were found to be abundant in glioblastomas. Glioblastoma-derived microvesicles were also found to potently promote angiogenic features in primary human brain microvascular endothelial cells (HBMVEC) in culture. This angiogenic effect was mediated at least in part through angiogenic proteins present in the microvesicles. The nucleic acids found within these microvesicles, as well as other contents of the microvesicles such as angiogenic proteins, can be used as valuable biomarkers for tumor diagnosis, characterization and prognosis by providing a genetic profile. Contents within these microvesicles can also be used to monitor tumor progression over time by analyzing if other mutations are acquired during tumor progression as well as if the levels of certain mutations are becoming increased or decreased over time or over a course of treatment

Certain aspects of the present invention are based on the finding that microvesicles are secreted by tumor cells and circulating in bodily fluids. The number of microvesicles increases as the tumor grows. The concentration of the microvesicles in bodily fluids is proportional to the corresponding tumor load. The bigger the tumor load, the higher the concentration of microvesicles in bodily fluids.

Certain aspects of the present invention are based on another surprising finding that most of the extracellular RNAs in bodily fluid of a subject are contained within microvesicles and thus protected from degradation by ribonucleases. As shown in Example 3, more than 90% of extracellular RNA in total serum can be recovered in microvesicles.

One aspect of the present invention relates to methods for detecting, diagnosing, monitoring, treating or evaluating a disease or other medical condition in a subject by determining the concentration of microvesicles in a biological sample. The determination may be performed using the biological sample without first isolating the microvesicles or by isolating the microvesicles first.

Another aspect of the present invention relates to methods for detecting, diagnosing, monitoring, treating or evaluating a disease or other medical condition in a subject comprising the steps of, isolating exosomes from a bodily fluid of a subject, and analyzing one or more nucleic acids contained within the exosomes. The nucleic acids are analyzed qualitatively and/or quantitatively, and the results are compared to results expected or obtained for one or more other subjects who have or do not have the disease or other medical condition. The presence of a difference in microvesicular nucleic acid content of the subject, as compared to that of one or more other individuals, can indicate the presence or absence of, the progression of (e.g., changes of tumor size and tumor malignancy), or the susceptibility to a disease or other medical condition in the subject.

Indeed, the isolation methods and techniques described herein provide the following heretofore unrealized advantages: 1) the opportunity to selectively analyze disease- or tumor-specific nucleic acids, which may be realized by isolating disease- or tumor-specific microvesicles apart from other microvesicles within the fluid sample; 2) significantly higher yield of nucleic acid species with higher sequence integrity as compared to the yield/integrity obtained by extracting nucleic acids directly from the fluid sample; 3) scalability, e.g. to detect nucleic acids expressed at low levels, the sensitivity can be increased by pelleting more microvesicles from a larger volume of serum; 4) purer nucleic acids in that protein and lipids, debris from dead cells, and other potential contaminants and PCR inhibitors are excluded from the microvesicle pellets before the nucleic acid extraction step; and 5) more choices in nucleic acid extraction methods as microvesicle pellets are of much smaller volume than that of the starting serum, making it possible to extract nucleic acids from these microvesicle pellets using small volume column filters.

The microvesicles are preferably isolated from a sample taken of a bodily fluid from a subject. As used herein, a “bodily fluid” refers to a sample of fluid isolated from anywhere in the body of the subject, preferably a peripheral location, including but not limited to, for example, blood, plasma, serum, urine, sputum, spinal fluid, pleural fluid, nipple aspirates, lymph fluid, fluid of the respiratory, intestinal, and genitourinary tracts, tear fluid, saliva, breast milk, fluid from the lymphatic system, semen, cerebrospinal fluid, intra-organ system fluid, ascitic fluid, tumor cyst fluid, amniotic fluid and combinations thereof.

The term “subject” is intended to include all animals shown to or expected to have microvesicles. In particular embodiments, the subject is a mammal, a human or nonhuman primate, a dog, a cat, a horse, a cow, other farm animals, or a rodent (e.g. mice, rats, guinea pig. etc.). The term “subject” and “individual” are used interchangeably herein.

Methods of isolating microvesicles from a biological sample are known in the art. For example, a method of differential centrifugation is described in a paper by Raposo et al. (Raposo et al., 1996), and similar methods are detailed in the Examples section herein. Methods of anion exchange and/or gel permeation chromatography are described in U.S. Pat. Nos. 6,899,863 and 6,812,023. Methods of sucrose density gradients or organelle electrophoresis are described in U.S. Pat. No. 7,198,923. A method of magnetic activated cell sorting (MACS) is described in (Taylor and Gercel-Taylor, 2008). A method of nanomembrane ultrafiltration concentrator is described in (Cheruvanky et al., 2007). Preferably, microvesicles can be identified and isolated from bodily fluid of a subject by a newly developed microchip technology that uses a unique microfluidic platform to efficiently and selectively separate tumor derived microvesicles. This technology, as described in a paper by Nagrath et al. (Nagrath et al., 2007), can be adapted to identify and separate microvesicles using similar principles of capture and separation as taught in the paper. Each of the foregoing references is incorporated by reference herein for its teaching of these methods.

In one embodiment, the microvesicles isolated from a bodily fluid are enriched for those originating from a specific cell type, for example, lung, pancreas, stomach, intestine, bladder, kidney, ovary, testis, skin, colorectal, breast, prostate, brain, esophagus, liver, placenta, fetus cells. Because the microvesicles often carry surface molecules such as antigens from their donor cells, surface molecules may be used to identify, isolate and/or enrich for microvesicles from a specific donor cell type (Al-Nedawi et al., 2008; Taylor and Gercel-Taylor, 2008). In this way, microvesicles originating from distinct cell populations can be analyzed for their nucleic acid content. For example, tumor (malignant and non-malignant) microvesicles carry tumor-associated surface antigens and may be detected, isolated and/or enriched via these specific tumor-associated surface antigens. In one example, the surface antigen is epithelial-cell-adhesion-molecule (EpCAM), which is specific to microvesicles from carcinomas of lung, colorectal, breast, prostate, head and neck, and hepatic origin, but not of hematological cell origin (Balzar et al., 1999; Went et al., 2004). In another example, the surface antigen is CD24, which is a glycoprotein specific to urine microvesicles (Keller et al., 2007). In yet another example, the surface antigen is selected from a group of molecules CD70, carcinoembryonic antigen (CEA), EGFR, EGFRvIII and other variants, Fas ligand, TRAIL, tranferrin receptor, p38.5, p97 and HSP72. Additionally, tumor specific microvesicles may be characterized by the lack of surface markers, such as CD80 and CD86.

The isolation of microvesicles from specific cell types can be accomplished, for example, by using antibodies, aptamers, aptamer analogs or molecularly imprinted polymers specific for a desired surface antigen. In one embodiment, the surface antigen is specific for a cancer type. In another embodiment, the surface antigen is specific for a cell type which is not necessarily cancerous. One example of a method of microvesicle separation based on cell surface antigen is provided in U.S. Pat. No. 7,198,923. As described in, e.g., U.S. Pat. Nos. 5,840,867 and 5,582,981, WO/2003/050290 and a publication by Johnson et al. (Johnson et al., 2008), aptamers and their analogs specifically bind surface molecules and can be used as a separation tool for retrieving cell type-specific microvesicles. Molecularly imprinted polymers also specifically recognize surface molecules as described in, e.g., U.S. Pat. Nos. 6,525,154, 7,332,553 and 7,384,589 and a publication by Bossi et al. (Bossi et al., 2007) and are a tool for retrieving and isolating cell type-specific microvesicles. Each of the foregoing reference is incorporated herein for its teaching of these methods.

It may be beneficial or otherwise desirable to extract the nucleic acid from the exosomes prior to the analysis. Nucleic acid molecules can be isolated from a microvesicle using any number of procedures, which are well-known in the art, the particular isolation procedure chosen being appropriate for the particular biological sample. Examples of methods for extraction are provided in the Examples section herein. In some instances, with some techniques, it may also be possible to analyze the nucleic acid without extraction from the microvesicle.

In one embodiment, the extracted nucleic acids, including DNA and/or RNA, are analyzed directly without an amplification step. Direct analysis may be performed with different methods including, but not limited to, the nanostring technology. NanoString technology enables identification and quantification of individual target molecules in a biological sample by attaching a color coded fluorescent reporter to each target molecule. This approach is similar to the concept of measuring inventory by scanning barcodes. Reporters can be made with hundreds or even thousands of different codes allowing for highly multiplexed analysis. The technology is described in a publication by Geiss et al. (Geiss et al., 2008) and is incorporated herein by reference for this teaching.

In another embodiment, it may be beneficial or otherwise desirable to amplify the nucleic acid of the microvesicle prior to analyzing it. Methods of nucleic acid amplification are commonly used and generally known in the art, many examples of which are described herein. If desired, the amplification can be performed such that it is quantitative. Quantitative amplification will allow quantitative determination of relative amounts of the various nucleic acids, to generate a profile as described below.

In one embodiment, the extracted nucleic acid is RNA. RNAs are then preferably reverse-transcribed into complementary DNAs before further amplification. Such reverse transcription may be performed alone or in combination with an amplification step. One example of a method combining reverse transcription and amplification steps is reverse transcription polymerase chain reaction (RT-PCR), which may be further modified to be quantitative, e.g., quantitative RT-PCR as described in U.S. Pat. No. 5,639,606, which is incorporated herein by reference for this teaching.

Nucleic acid amplification methods include, without limitation, polymerase chain reaction (PCR) (U.S. Pat. No. 5,219,727) and its variants such as in situ polymerase chain reaction (U.S. Pat. No. 5,538,871), quantitative polymerase chain reaction (U.S. Pat. No. 5,219,727), nested polymerase chain reaction (U.S. Pat. No. 5,556,773), self sustained sequence replication and its variants (Guatelli et al., 1990), transcriptional amplification system and its variants (Kwoh et al., 1989), Qb Replicase and its variants (Miele et al., 1983), cold-PCR (Li et al., 2008) or any other nucleic acid amplification methods, followed by the detection of the amplified molecules using techniques well known to those of skill in the art. Especially useful are those detection schemes designed for the detection of nucleic acid molecules if such molecules are present in very low numbers. The foregoing references are incorporated herein for their teachings of these methods.

The analysis of nucleic acids present in the microvesicles is quantitative and/or qualitative. For quantitative analysis, the amounts (expression levels), either relative or absolute, of specific nucleic acids of interest within the microvesicles are measured with methods known in the art (described below). For qualitative analysis, the species of specific nucleic acids of interest within the microvesicles, whether wild type or variants, are identified with methods known in the art (described below).

“Genetic aberrations” is used herein to refer to the nucleic acid amounts as well as nucleic acid variants within the microvesicles. Specifically, genetic aberrations include, without limitation, over-expression of a gene (e.g., oncogenes) or a panel of genes, under-expression of a gene (e.g., tumor suppressor genes such as p53 or RB) or a panel of genes, alternative production of splice variants of a gene or a panel of genes, gene copy number variants (CNV) (e.g. DNA double minutes) (Hahn, 1993), nucleic acid modifications (e.g., methylation, acetylation and phosphorylations), single nucleotide polymorphisms (SNPs), chromosomal rearrangements (e.g., inversions, deletions and duplications), and mutations (insertions, deletions, duplications, missense, nonsense, synonymous or any other nucleotide changes) of a gene or a panel of genes, which mutations, in many cases, ultimately affect the activity and function of the gene products, lead to alternative transcriptional splicing variants and/or changes of gene expression level.

The determination of such genetic aberrations can be performed by a variety of techniques known to the skilled practitioner. For example, expression levels of nucleic acids, alternative splicing variants, chromosome rearrangement and gene copy numbers can be determined by microarray analysis (U.S. Pat. Nos. 6,913,879, 7,364,848, 7,378,245, 6,893,837 and 6,004,755) and quantitative PCR. Particularly, copy number changes may be detected with the Illumina Infinium II whole genome genotyping assay or Agilent Human Genome CGH Microarray (Steemers et al., 2006). Nucleic acid modifications can be assayed by methods described in, e.g., U.S. Pat. No. 7,186,512 and patent publication WO/2003/023065. Particularly, methylation profiles may be determined by Illumina DNA Methylation OMA003 Cancer Panel. SNPs and mutations can be detected by hybridization with allele-specific probes, enzymatic mutation detection, chemical cleavage of mismatched heteroduplex (Cotton et al., 1988), ribonuclease cleavage of mismatched bases (Myers et al., 1985), mass spectrometry (U.S. Pat. Nos. 6,994,960, 7,074,563, and 7,198,893), nucleic acid sequencing, single strand conformation polymorphism (SSCP) (Orita et al., 1989), denaturing gradient gel electrophoresis (DGGE)(Fischer and Lerman, 1979a; Fischer and Lerman, 1979b), temperature gradient gel electrophoresis (TGGE) (Fischer and Lerman, 1979a; Fischer and Lerman, 1979b), restriction fragment length polymorphisms (RFLP) (Kan and Dozy, 1978a; Kan and Dozy, 1978b), oligonucleotide ligation assay (OLA), allele-specific PCR (ASPCR) (U.S. Pat. No. 5,639,611), ligation chain reaction (LCR) and its variants (Abravaya et al., 1995; Landegren et al., 1988; Nakazawa et al., 1994), flow-cytometric heteroduplex analysis (WO/2006/113590) and combinations/modifications thereof. Notably, gene expression levels may be determined by the serial analysis of gene expression (SAGE) technique (Velculescu et al., 1995). In general, the methods for analyzing genetic aberrations are reported in numerous publications, not limited to those cited herein, and are available to skilled practitioners. The appropriate method of analysis will depend upon the specific goals of the analysis, the condition/history of the patient, and the specific cancer(s), diseases or other medical conditions to be detected, monitored or treated. The forgoing references are incorporated herein for their teachings of these methods.

A variety of genetic aberrations have been identified to occur and/or contribute to the initial generation or progression of cancer. Examples of genes which are commonly up-regulated (i.e. over-expressed) in cancer are provided in Table 4 (cancers of different types) and Table 6 (pancreatic cancer). Examples of microRNAs which are up-regulated in brain tumor are provided in Table 8. In one embodiment of the invention, there is an increase in the nucleic acid expression level of a gene listed in Table 4 and/or Table 6 and/or of a microRNA listed in Table 8. Examples of genes which are commonly down-regulated (e.g. under-expressed) in cancer are provided in Table 5 (cancers of different types) and Table 7 (pancreatic cancer). Examples of microRNAs which are down-regulated in brain tumor are provided in Table 9. In one embodiment of the invention, there is a decrease in the nucleic acid expression level of a gene listed in Table 5 and/or Table 7 and/or a microRNA listed in Table 9. Examples of genes which are commonly under expressed, or over expressed in brain tumors are reviewed in (Furnari et al., 2007), and this subject matter is incorporated herein by reference. With respect to the development of brain tumors, RB and p53 are often down-regulated to otherwise decrease their tumor suppressive activity. Therefore, in these embodiments, the presence or absence of an increase or decrease in the nucleic acid expression level of a gene(s) and/or a microRNA(s) whose disregulated expression level is specific to a type of cancer can be used to indicate the presence or absence of the type of cancer in the subject.

Likewise, nucleic acid variants, e.g., DNA or RNA modifications, single nucleotide polymorphisms (SNPs) and mutations (e.g., missense, nonsense, insertions, deletions, duplications) may also be analyzed within microvesicles from bodily fluid of a subject, including pregnant females where microvesicles derived from the fetus may be in serum as well as amniotic fluid. Non-limiting examples are provided in Table 3. In yet a further embodiment, the nucleotide variant is in the EGFR gene. In a still further embodiment, the nucleotide variant is the EGFRvIII mutation/variant. The terms “EGFR”, “epidermal growth factor receptor” and “ErbB1” are used interchangeably in the art, for example as described in a paper by Carpenter (Carpenter, 1987). With respect to the development of brain tumors, RB, PTEN, p16, p21 and p53 are often mutated to otherwise decrease their tumor suppressive activity. Examples of specific mutations in specific forms of brain tumors are discussed in a paper by Furnari et al. (Furnari et al., 2007), and this subject matter is incorporated herein by reference.

In addition, more genetic aberrations associated with cancers have been identified recently in a few ongoing research projects. For example, the Cancer Genome Atlas (TCGA) program is exploring a spectrum of genomic changes involved in human cancers. The results of this project and other similar research efforts are published and incorporated herein by reference (Jones et al., 2008; McLendon et al., 2008; Parsons et al., 2008; Wood et al., 2007). Specifically, these research projects have identified genetic aberrations, such as mutations (e.g., missense, nonsense, insertions, deletions and duplications), gene expression level variations (mRNA or microRNA), copy number variations and nucleic acid modification (e.g. methylation), in human glioblastoma, pancreatic cancer, breast cancer and/or colorectal cancer. The genes most frequently mutated in these cancers are listed in Table 11 and Table 12 (glioblastoma), Table 13 (pancreatic cancer), Table 14 (breast cancer) and Table 15 (colorectal cancer). The genetic aberrations in these genes, and in fact any genes which contain any genetic aberrations in a cancer, are targets that may be selected for use in diagnosing and/or monitoring cancer by the methods described herein.

Detection of one or more nucleotide variants can be accomplished by performing a nucleotide variant screen on the nucleic acids within the microvesicles. Such a screen can be as wide or narrow as determined necessary or desirable by the skilled practitioner. It can be a wide screen (set up to detect all possible nucleotide variants in genes known to be associated with one or more cancers or disease states). Where one specific cancer or disease is suspected or known to exist, the screen can be specific to that cancer or disease. One example is a brain tumor/brain cancer screen (e.g., set up to detect all possible nucleotide variants in genes associated with various clinically distinct subtypes of brain cancer or known drug-resistant or drug-sensitive mutations of that cancer).

In one embodiment, the analysis is of a profile of the amounts (levels) of specific nucleic acids present in the microvesicle, herein referred to as a “quantitative nucleic acid profile” of the microvesicles. In another embodiment, the analysis is of a profile of the species of specific nucleic acids present in the microvesicles (both wild type as well as variants), herein referred to as a “nucleic acid species profile.” A term used herein to refer to a combination of these types of profiles is “genetic profile” which refers to the determination of the presence or absence of nucleotide species, variants and also increases or decreases in nucleic acid levels.

Once generated, these genetic profiles of the microvesicles are compared to those expected in, or otherwise derived from a healthy normal individual. A profile can be a genome wide profile (set up to detect all possible expressed genes or DNA sequences). It can be narrower as well, such as a cancer wide profile (set up to detect all possible genes or nucleic acids derived therefrom, or known to be associated with one or more cancers). Where one specific cancer is suspected or known to exist, the profile can be specific to that cancer (e.g., set up to detect all possible genes or nucleic acids derived therefrom, associated with various clinically distinct subtypes of that cancer or known drug-resistant or sensitive mutations of that cancer).

Which nucleic acids are to be amplified and/or analyzed can be selected by the skilled practitioner. The entire nucleic acid content of the exosomes or only a subset of specific nucleic acids which are likely or suspected of being influenced by the presence of a disease or other medical condition such as cancer, can be amplified and/or analyzed. The identification of a nucleic acid aberration(s) in the analyzed microvesicle nucleic acid can be used to diagnose the subject for the presence of a disease such as cancer, hereditary diseases or viral infection with which that aberration(s) is associated. For instance, analysis for the presence or absence of one or more nucleic acid variants of a gene specific to a cancer (e.g. the EGFRvIII mutation) can indicate the cancer's presence in the individual. Alternatively, or in addition, analysis of nucleic acids for an increase or decrease in nucleic acid levels specific to a cancer can indicate the presence of the cancer in the individual (e.g., a relative increase in EGFR nucleic acid, or a relative decrease in a tumor suppressor gene such as p53).

In one embodiment, mutations of a gene which is associated with a disease such as cancer (e.g. via nucleotide variants, over-expression or under-expression) are detected by analysis of nucleic acids in microvesicles, which nucleic acids are derived from the genome itself in the cell of origin or exogenous genes introduced through viruses. The nucleic acid sequences may be complete or partial, as both are expected to yield useful information in diagnosis and prognosis of a disease. The sequences may be sense or anti-sense to the actual gene or transcribed sequences. The skilled practitioner will be able to devise detection methods for a nucleotide variance from either the sense or anti-sense nucleic acids which may be present in a microvesicle. Many such methods involve the use of probes which are specific for the nucleotide sequences which directly flank, or contain the nucleotide variances. Such probes can be designed by the skilled practitioner given the knowledge of the gene sequences and the location of the nucleic acid variants within the gene. Such probes can be used to isolate, amplify, and/or actually hybridize to detect the nucleic acid variants, as described in the art and herein.

Determining the presence or absence of a particular nucleotide variant or plurality of variants in the nucleic acid within microvesicles from a subject can be performed in a variety of ways. A variety of methods are available for such analysis, including, but not limited to, PCR, hybridization with allele-specific probes, enzymatic mutation detection, chemical cleavage of mismatches, mass spectrometry or DNA sequencing, including minisequencing. In particular embodiments, hybridization with allele specific probes can be conducted in two formats: 1) allele specific oligonucleotides bound to a solid phase (glass, silicon, nylon membranes) and the labeled sample in solution, as in many DNA chip applications, or 2) bound sample (often cloned DNA or PCR amplified DNA) and labeled oligonucleotides in solution (either allele specific or short so as to allow sequencing by hybridization). Diagnostic tests may involve a panel of variances, often on a solid support, which enables the simultaneous determination of more than one variance. In another embodiment, determining the presence of at least one nucleic acid variance in the microvesicle nucleic acid entails a haplotyping test. Methods of determining haplotypes are known to those of skill in the art, as for example, in WO 00/04194.

In one embodiment, the determination of the presence or absence of a nucleic acid variant(s) involves determining the sequence of the variant site or sites (the exact location within the sequence where the nucleic acid variation from the norm occurs) by methods such as polymerase chain reaction (PCR), chain terminating DNA sequencing (U.S. Pat. No. 5,547,859), minisequencing (Fiorentino et al., 2003), oligonucleotide hybridization, pyrosequencing, Illumina genome analyzer, deep sequencing, mass spectrometry or other nucleic acid sequence detection methods. Methods for detecting nucleic acid variants are well known in the art and disclosed in WO 00/04194, incorporated herein by reference. In an exemplary method, the diagnostic test comprises amplifying a segment of DNA or RNA (generally after converting the RNA to complementary DNA) spanning one or more known variants in the desired gene sequence. This amplified segment is then sequenced and/or subjected to electrophoresis in order to identify nucleotide variants in the amplified segment.

In one embodiment, the invention provides a method of screening for nucleotide variants in the nucleic acid of microvesicles isolated as described herein. This can be achieved, for example, by PCR or, alternatively, in a ligation chain reaction (LCR) (Abravaya et al., 1995; Landegren et al., 1988; Nakazawa et al., 1994). LCR can be particularly useful for detecting point mutations in a gene of interest (Abravaya et al., 1995). The LCR method comprises the steps of designing degenerate primers for amplifying the target sequence, the primers corresponding to one or more conserved regions of the nucleic acid corresponding to the gene of interest, amplifying PCR products with the primers using, as a template, a nucleic acid obtained from a microvesicle, and analyzing the PCR products. Comparison of the PCR products of the microvesicle nucleic acid to a control sample (either having the nucleotide variant or not) indicates variants in the microvesicle nucleic acid. The change can be either an absence or presence of a nucleotide variant in the microvesicle nucleic acid, depending upon the control.

Analysis of amplification products can be performed using any method capable of separating the amplification products according to their size, including automated and manual gel electrophoresis, mass spectrometry, and the like.

Alternatively, the amplification products can be analyzed based on sequence differences, using SSCP, DGGE, TGGE, chemical cleavage, OLA, restriction fragment length polymorphisms as well as hybridization, for example, nucleic acid microarrays.

The methods of nucleic acid isolation, amplification and analysis are routine for one skilled in the art and examples of protocols can be found, for example, in Molecular Cloning: A Laboratory Manual (3-Volume Set) Ed. Joseph Sambrook, David W. Russel, and Joe Sambrook, Cold Spring Harbor Laboratory, 3rd edition (Jan. 15, 2001), ISBN: 0879695773. A particular useful protocol source for methods used in PCR amplification is PCR Basics: From Background to Bench by Springer Verlag; 1st edition (Oct. 15, 2000), ISBN: 0387916008.

Many methods of diagnosis performed on a tumor biopsy sample can be performed with microvesicles since tumor cells, as well as some normal cells are known to shed microvesicles into bodily fluid and the genetic aberrations within these microvesicles reflect those within tumor cells as demonstrated herein. Furthermore, methods of diagnosis using microvesicles have characteristics that are absent in methods of diagnosis performed directly on a tumor biopsy sample. For example, one particular advantage of the analysis of microvesicular nucleic acids, as opposed to other forms of sampling of tumor/cancer nucleic acid, is the availability for analysis of tumor/cancer nucleic acids derived from all foci of a tumor or genetically heterogeneous tumors present in an individual. Biopsy samples are limited in that they provide information only about the specific focus of the tumor from which the biopsy is obtained. Different tumorous/cancerous foci found within the body, or even within a single tumor often have different genetic profiles and are not analyzed in a standard biopsy. However, analysis of the microvesicular nucleic acids from an individual presumably provides a sampling of all foci within an individual. This provides valuable information with respect to recommended treatments, treatment effectiveness, disease prognosis, and analysis of disease recurrence, which cannot be provided by a simple biopsy.

Identification of genetic aberrations associated with specific diseases and/or medical conditions by the methods described herein can also be used for prognosis and treatment decisions of an individual diagnosed with a disease or other medical condition such as cancer. Identification of the genetic basis of a disease and/or medical condition provides useful information guiding the treatment of the disease and/or medical condition. For example, many forms of chemotherapy have been shown to be more effective on cancers with specific genetic abnormalities/aberrations. One example is the effectiveness of EGFR-targeting treatments with medicines, such as the kinase inhibitors gefitinib and erlotinib. Such treatment have been shown to be more effective on cancer cells whose EGFR gene harbors specific nucleotide mutations in the kinase domain of EGFR protein (U.S. Patent publication 20060147959). In other words, the presence of at least one of the identified nucleotide variants in the kinase domain of EGFR nucleic acid message indicates that a patient will likely benefit from treatment with the EGFR-targeting compound gefitinib or erlotinib. Such nucleotide variants can be identified in nucleic acids present in microvesicles by the methods described herein, as it has been demonstrated that EGFR transcripts of tumor origin are isolated from microvesicles in bodily fluid.

Genetic aberrations in other genes have also been found to influence the effectiveness of treatments. As disclosed in the publication by Furnari et al. (Furnari et al., 2007), mutations in a variety of genes affect the effectiveness of specific medicines used in chemotherapy for treating brain tumors. The identification of these genetic aberrations in the nucleic acids within microvesicles will guide the selection of proper treatment plans.

As such, aspects of the present invention relate to a method for monitoring disease (e.g. cancer) progression in a subject, and also to a method for monitoring disease recurrence in an individual. These methods comprise the steps of isolating microvesicles from a bodily fluid of an individual, as discussed herein, and analyzing nucleic acid within the microvesicles as discussed herein (e.g. to create a genetic profile of the microvesicles). The presence/absence of a certain genetic aberration/profile is used to indicate the presence/absence of the disease (e.g. cancer) in the subject as discussed herein. The process is performed periodically over time, and the results reviewed, to monitor the progression or regression of the disease, or to determine recurrence of the disease. Put another way, a change in the genetic profile indicates a change in the disease state in the subject. The period of time to elapse between sampling of microvesicles from the subject, for performance of the isolation and analysis of the microvesicle, will depend upon the circumstances of the subject, and is to be determined by the skilled practitioner. Such a method would prove extremely beneficial when analyzing a nucleic acid from a gene that is associated with the therapy undergone by the subject. For example, a gene which is targeted by the therapy can be monitored for the development of mutations which make it resistant to the therapy, upon which time the therapy can be modified accordingly. The monitored gene may also be one which indicates specific responsiveness to a specific therapy.

Aspects of the present invention also relate to the fact that a variety of non-cancer diseases and/or medical conditions also have genetic links and/or causes, and such diseases and/or medical conditions can likewise be diagnosed and/or monitored by the methods described herein. Many such diseases are metabolic, infectious or degenerative in nature. One such disease is diabetes (e.g. diabetes insipidus) in which the vasopressin type 2 receptor (V2R) is modified. Another such disease is kidney fibrosis in which the genetic profiles for the genes of collagens, fibronectin and TGF-β are changed. Changes in the genetic profile due to substance abuse (e.g. a steroid or drug use), viral and/or bacterial infection, and hereditary disease states can likewise be detected by the methods described herein.

Diseases or other medical conditions for which the inventions described herein are applicable include, but are not limited to, nephropathy, diabetes insipidus, diabetes type I, diabetes II, renal disease glomerulonephritis, bacterial or viral glomerulonephritides, IgA nephropathy, Henoch-Schonlein Purpura, membranoproliferative glomerulonephritis, membranous nephropathy, Sjogren's syndrome, nephrotic syndrome minimal change disease, focal glomerulosclerosis and related disorders, acute renal failure, acute tubulointerstitial nephritis, pyelonephritis, GU tract inflammatory disease, Pre-clampsia, renal graft rejection, leprosy, reflux nephropathy, nephrolithiasis, genetic renal disease, medullary cystic, medullar sponge, polycystic kidney disease, autosomal dominant polycystic kidney disease, autosomal recessive polycystic kidney disease, tuberous sclerosis, von Hippel-Lindau disease, familial thin-glomerular basement membrane disease, collagen III glomerulopathy, fibronectin glomerulopathy, Alport's syndrome, Fabry's disease, Nail-Patella Syndrome, congenital urologic anomalies, monoclonal gammopathies, multiple myeloma, amyloidosis and related disorders, febrile illness, familial Mediterranean fever, HIV infection-AIDS, inflammatory disease, systemic vasculitides, polyarteritis nodosa, Wegener's granulomatosis, polyarteritis, necrotizing and crecentic glomerulonephritis, polymyositis-dermatomyositis, pancreatitis, rheumatoid arthritis, systemic lupus erythematosus, gout, blood disorders, sickle cell disease, thrombotic thrombocytopenia purpura, Fanconi's syndrome, transplantation, acute kidney injury, irritable bowel syndrome, hemolytic-uremic syndrome, acute corticol necrosis, renal thromboembolism, trauma and surgery, extensive injury, burns, abdominal and vascular surgery, induction of anesthesia, side effect of use of drugs or drug abuse, circulatory disease myocardial infarction, cardiac failure, peripheral vascular disease, hypertension, coronary heart disease, non-atherosclerotic cardiovascular disease, atherosclerotic cardiovascular disease, skin disease, soriasis, systemic sclerosis, respiratory disease, COPD, obstructive sleep apnoea, hypoia at high altitude or erdocrine disease, acromegaly, diabetes mellitus, or diabetes insipidus.

Selection of an individual from whom the microvesicles are isolated is performed by the skilled practitioner based upon analysis of one or more of a variety of factors. Such factors for consideration are whether the subject has a family history of a specific disease (e.g. a cancer), has a genetic predisposition for such a disease, has an increased risk for such a disease due to family history, genetic predisposition, other disease or physical symptoms which indicate a predisposition, or environmental reasons. Environmental reasons include lifestyle, exposure to agents which cause or contribute to the disease such as in the air, land, water or diet. In addition, having previously had the disease, being currently diagnosed with the disease prior to therapy or after therapy, being currently treated for the disease (undergoing therapy), being in remission or recovery from the disease, are other reasons to select an individual for performing the methods.

The methods described herein are optionally performed with the additional step of selecting a gene or nucleic acid for analysis, prior to the analysis step. This selection can be based on any predispositions of the subject, or any previous exposures or diagnosis, or therapeutic treatments experienced or concurrently undergone by the subject.

The cancer diagnosed, monitored or otherwise profiled, can be any kind of cancer. This includes, without limitation, epithelial cell cancers such as lung, ovarian, cervical, endometrial, breast, brain, colon and prostate cancers. Also included are gastrointestinal cancer, head and neck cancer, non-small cell lung cancer, cancer of the nervous system, kidney cancer, retina cancer, skin cancer, liver cancer, pancreatic cancer, genital-urinary cancer and bladder cancer, melanoma, and leukemia. In addition, the methods and compositions of the present invention are equally applicable to detection, diagnosis and prognosis of non-malignant tumors in an individual (e.g. neurofibromas, meningiomas and schwannomas).

In one embodiment, the cancer is brain cancer. Types of brain tumors and cancer are well known in the art. Glioma is a general name for tumors that arise from the glial (supportive) tissue of the brain. Gliomas are the most common primary brain tumors. Astrocytomas, ependymomas, oligodendrogliomas, and tumors with mixtures of two or more cell types, called mixed gliomas, are the most common gliomas. The following are other common types of brain tumors: Acoustic Neuroma (Neurilemmoma, Schwannoma. Neurinoma), Adenoma, Astracytoma, Low-Grade Astrocytoma, giant cell astrocytomas, Mid- and High-Grade Astrocytoma, Recurrent tumors, Brain Stem Glioma, Chordoma, Choroid Plexus Papilloma, CNS Lymphoma (Primary Malignant Lymphoma), Cysts, Dermoid cysts, Epidermoid cysts, Craniopharyngioma, Ependymoma Anaplastic ependymoma, Gangliocytoma (Ganglioneuroma), Ganglioglioma, Glioblastoma Multiforme (GBM), Malignant Astracytoma, Glioma, Hemangioblastoma, Inoperable Brain Tumors, Lymphoma, Medulloblastoma (MDL), Meningioma, Metastatic Brain Tumors, Mixed Glioma, Neurofibromatosis, Oligodendroglioma. Optic Nerve Glioma, Pineal Region Tumors, Pituitary Adenoma, PNET (Primitive Neuroectodermal Tumor), Spinal Tumors, Subependymoma, and Tuberous Sclerosis (Bourneville's Disease).

In addition to identifying previously known nucleic acid aberrations (as associated with diseases), the methods of the present invention can be used to identify previously unidentified nucleic acid sequences/modifications (e.g. post transcriptional modifications) whose aberrations are associated with a certain disease and/or medical condition. This is accomplished, for example, by analysis of the nucleic acid within microvesicles from a bodily fluid of one or more subjects with a given disease/medical condition (e.g. a clinical type or subtype of cancer) and comparison to the nucleic acid within microvesicles of one or more subjects without the given disease/medical condition, to identify differences in their nucleic acid content. The differences may be any genetic aberrations including, without limitation, expression level of the nucleic acid, alternative splice variants, gene copy number variants (CNV), modifications of the nucleic acid, single nucleotide polymorphisms (SNPs), and mutations (insertions, deletions or single nucleotide changes) of the nucleic acid. Once a difference in a genetic parameter of a particular nucleic acid is identified for a certain disease, further studies involving a clinically and statistically significant number of subjects may be carried out to establish the correlation between the genetic aberration of the particular nucleic acid and the disease. The analysis of genetic aberrations can be done by one or more methods described herein, as determined appropriate by the skilled practitioner.

Exosomes as Delivery Vehicles

Aspects of the present invention also relate to the actual microvesicles described herein. In one embodiment, the invention is an isolated microvesicle as described herein, isolated from an individual. In one embodiment, the microvesicle is produced by a cell within the brain of the individual (e.g. a tumor or non-tumor cell). In another embodiment, the microvesicle is isolated from a bodily fluid of an individual, as described herein. Methods of isolation are described herein.

Another aspect of the invention relates to the finding that isolated microvesicles from human glioblastoma cells contain mRNAs, miRNAs and angiogenic proteins. Such glioblastoma microvesicles were taken up by primary human brain endothelial cells, likely via an endocytotic mechanism, and a reporter protein mRNA incorporated into the microvesicles was translated in those cells. This indicates that messages delivered by microvesicles can change the genetic and/or translational profile of a target cell (a cell which takes up a microvesicle). The microvesicles also contained miRNAs which are known to be abundant in glioblastomas (Krichevsky et al, manuscript in preparation). Thus microvesicles derived from glioblastoma tumors function as delivery vehicles for mRNA, miRNA and proteins which can change the translational state of other cells via delivery of specific mRNA species, promote angiogenesis of endothelial cells, and stimulate tumor growth.

In one embodiment, microvesicles are depleted from a bodily fluid from a donor subject before said bodily fluid is delivered to a recipient subject. The donor subject may be a subject with an undetectable tumor and the microvesicles in the bodily fluid are derived from the tumor. The tumor microvesicles in the donor bodily fluid, if unremoved, would be harmful since the genetic materials and proteins in the microvesicle may promote unrestricted growth of cells in the recipient subject.

As such, another aspect of the invention is the use of the microvesicles identified herein to deliver a nucleic acid to a cell. In one embodiment, the cell is within the body of an individual. The method comprises administering a microvesicle(s) which contains the nucleic acid, or a cell that produces such microvesicles, to the individual such that the microvesicles contacts and/or enters the cell of the individual. The cell to which the nucleic acid gets delivered is referred to as the target cell.

The microvesicle can be engineered to contain a nucleic acid that it would not naturally contain (i.e. which is exogenous to the normal content of the microvesicle). This can be accomplished by physically inserting the nucleic acid into the microvesicles. Alternatively, a cell (e.g. grown in culture) can be engineered to target one or more specific nucleic acid into the exosome, and the exosome can be isolated from the cell. Alternatively, the engineered cell itself can be administered to the individual.

In one embodiment, the cell which produces the exosome for administration is of the same or similar origin or location in the body as the target cell. That is to say, for delivery of a microvesicle to a brain cell, the cell which produces the microvesicle would be a brain cell (e.g. a primary cell grown in culture). In another embodiment, the cell which produces the exosome is of a different cell type than the target cell. In one embodiment, the cell which produces the exosome is a type that is located proximally in the body to the target cell.

A nucleic acid sequence which can be delivered to a cell via an exosome can be RNA or DNA, and can be single or double stranded, and can be selected from a group comprising: nucleic acid encoding a protein of interest, oligonucleotides, nucleic acid analogues, for example peptide-nucleic acid (PNA), pseudo-complementary PNA (pc-PNA), locked nucleic acid (LNA) etc. Such nucleic acid sequences include, for example, but are not limited to, nucleic acid sequences encoding proteins, for example that act as transcriptional repressors, antisense molecules, ribozymes, small inhibitory nucleic acid sequences, for example but are not limited to RNAi, shRNA, siRNA, miRNA, antisense oligonucleotides, and combinations thereof.

Microvesicles isolated from a cell type are delivered to a recipient subject. Said microvesicles may benefit the recipient subject medically. For example, the angiogenesis and pro-proliferation effects of tumor exosomes may help the regeneration of injured tissues in the recipient subject. In one embodiment, the delivery means is by bodily fluid transfusion wherein microvesicles are added into a bodily fluid from a donor subject before said bodily fluid is delivered to a recipient subject.

In another embodiment, the microvesicle is an ingredient (e.g. the active ingredient in a pharmaceutically acceptable formulation suitable for administration to the subject (e.g. in the methods described herein). Generally this comprises a pharmaceutically acceptable carrier for the active ingredient. The specific carrier will depend upon a number of factors (e.g. the route of administration).

The “pharmaceutically acceptable carrier” means any pharmaceutically acceptable means to mix and/or deliver the targeted delivery composition to a subject. This includes a pharmaceutically acceptable material, composition or vehicle, such as a liquid or solid filler, diluent, excipient, solvent or encapsulating material, involved in carrying or transporting the subject agents from one organ, or portion of the body, to another organ, or portion of the body. Each carrier must be “acceptable” in the sense of being compatible with the other ingredients of the formulation and is compatible with administration to a subject, for example a human.

Administration to the subject can be either systemic or localized. This includes, without limitation, dispensing, delivering or applying an active compound (e.g. in a pharmaceutical formulation) to the subject by any suitable route for delivery of the active compound to the desired location in the subject, including delivery by either the parenteral or oral route, intramuscular injection, subcutaneous/intradermal injection, intravenous injection, buccal administration, transdermal delivery and administration by the rectal, colonic, vaginal, intranasal or respiratory tract route.

It should be understood that this invention is not limited to the particular methodologies, protocols and reagents, described herein and as such may vary. The terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present invention, which is defined solely by the claims.

In one respect, the present invention relates to the herein described compositions, methods, and respective components thereof, as essential to the invention, yet open to the inclusion of unspecified elements, essential or not (“comprising”). In some embodiments, other elements to be included in the description of the composition, method or respective component thereof are limited to those that do not materially affect the basic and novel characteristic(s) of the invention (“consisting essentially of”). This applies equally to steps within a described method as well as compositions and components therein. In other embodiments, the inventions, compositions, methods, and respective components thereof, described herein are intended to be exclusive of any element not deemed an essential element to the component, composition or method (“consisting of”).

Examples Examples 1-7. Tumor Cells Shed Microvesicles, which Contain RNAs, Including mRNAs and microRNAs, and that Microvesicles Contain More than 90% of the Extracellular RNA in Bodily Fluids Example 1: Microvesicles are Shed from Primary Human Glioblastoma Cells

Glioblastoma tissue was obtained from surgical resections and tumor cells were dissociated and cultured as monolayers. Specifically, brain tumor specimens from patients diagnosed by a neuropathologist as glioblastoma multiforme were taken directly from surgery and placed in cold sterile Neurobasal media (Invitrogen, Carlsbad, Calif., USA). The specimens were dissociated into single cells within 1 hr from the time of surgery using a Neural Tissue Dissociation Kit (Miltenyi Biotech, Berisch Gladbach, Germany) and plated in DMEM 5% dFBS supplemented with penicillin-streptomycin (10 IU ml⁻¹ and 10 μg ml⁻¹, respectively, Sigma-Aldrich, St Louis, Mo., USA). Because microvesicles can be found in the fetal bovine serum (FBS) traditionally used to cultivate cells, and these microvesicles contain substantial amounts of mRNA and miRNA, it was important to grow the tumor cells in media containing microvesicle-depleted FBS (dFBS). Cultured primary cells obtained from three glioblastoma tumors were found to produce microvesicles at both early and later passages (a passage is a cellular generation defined by the splitting of cells, which is a common cell culture technique and is necessary to keep the cells alive). The microvesicles were able to be detected by scanning electronmicroscopy (FIGS. 1a and 1b ) and transmission electronmicroscopy (FIG. 1f ). Briefly, human glioblastoma cells were placed on ornithine-coated cover-slips, fixed in 0.5× Karnovskys fixative and then washed 2×5 min (2 times with 5 min each) with PBS. The cells were dehydrated in 35% EtOH 10 min, 50% EtOH 2×10 min, 70% EtOH 2×10 min, 95% EtOH 2×10 min, and 100% EtOH 4×10 min. The cells were then transferred to critical point drying in a Tousimis SAMDR1-795 semi-automatic Critical Point Dryer followed by coating with chromium in a GATAN Model 681 High Resolution Ion Beam Coater. As shown in FIGS. 1a and 1b , tumor cells were covered with microvesicles varying in size from about 50-500 nm.

Example 2: Glioblastoma Microvesicles Contain RNA

To isolate microvesicles, glioblastoma cells at passage 1-15 were cultured in microvesicle-free media (DMEM containing 5% dFBS prepared by ultracentrifugation at 110,000×g for 16 hours to remove bovine microvesicles). The conditioned medium from 40 million cells was harvested after 48 hours. The microvesicles were purified by differential centrifugation. Specifically, glioblastoma conditioned medium was centrifuged for 10 min at 300×g to eliminate any cell contamination. Supernatants were further centrifuged for 20 min at 16,500×g and filtered through a 0.22 μm filter. Microvesicles were then pelleted by ultracentrifugation at 110,000×g for 70 min. The microvesicle pellets were washed in 13 ml PBS, pelleted again and resuspended in PBS.

Isolated microvesicles were measured for their total protein content using DC Protein Assay (Bio-Rad, Hercules, Calif., USA).

For the extraction of RNA from microvesicles, RNase A (Fermentas, Glen Burnie, Md., USA) at a final concentration of 100 μg/ml was added to suspensions of microvesicles and incubated for 15 min at 37° C. to get rid of RNA outside of the microvesicles and thus ensure that the extracted RNA would come from inside the microvesicles. Total RNA was then extracted from the microvesicles using the MirVana RNA isolation kit (Ambion, Austin Tex., USA) according to the manufacturer's protocol. After treatment with DNAse according to the manufacturer's protocol, the total RNA was quantified using a nanodrop ND-1000 instrument (Thermo Fischer Scientific, Wilmington, Del., USA).

Glioblastoma microvesicles were found to contain RNA and protein in a ratio of approximately 1:80 (μg RNA: μg protein). The average yield of proteins and RNAs isolated from microvesicles over a 48-hour period in culture was around 4 μg protein and 50 ng RNA/million cells.

To confirm that the RNA was contained inside the microvesicles, microvesicles were either exposed to RNase A or mock treatment before RNA extraction (FIG. 1c ). There was never more than a 7% decrease in RNA content following RNase treatment. Thus, it appears that almost all of the extracellular RNA from the media is contained within the microvesicles and is thereby protected from external RNases by the surrounding vesicular membrane.

Total RNA from microvesicles and their donor cells were analyzed with a Bioanalyzer, showing that the microvesicles contain a broad range of RNA sizes consistent with a variety of mRNAs and miRNAs, but lack 18S and 28S the ribosomal RNA peaks characteristic of cellular RNA (FIGS. 1d and 1e ).

Example 3: Microvesicles Contain DNA

To test if microvesicles also contain DNA, exosomes were isolated as mentioned in Example 2 and then treated with DNase before being lysed to release contents. The DNase treatment step was to remove DNA outside of the exosomes so that only DNA residing inside the exosomes was extracted. Specifically, the DNase treatment was performed using the DNA-free kit from Ambion according to manufacturer's recommendations (Catalog#AM1906). For the DNA purification step, an aliquot of isolated exosomes was lysed in 300 μl lysis buffer that was part of the MirVana RNA isolation kit (Ambion) and the DNAs were purified from the lysed mixture using a DNA purification kit (Qiagen) according to the manufacturer's recommendation.

To examine whether the extracted DNA contains common genes, PCRs were performed using primer pairs specific to GAPDH, Human endogenous retrovirus K, Tenascin-c and Line-1. For the GAPDH gene, the following primers were used: Forw3GAPDHnew (SEQ ID NO: 1) and Rev3GAPDHnew (SEQ ID NO: 2). The primer pair amplifies a 112 bp amplicon if the template is a spliced GAPDH cDNA and a 216 bp amplicon if the template is an un-spliced genomic GAPDH DNA. In one experiment, isolated exosomes were treated with DNase before being lysed for DNA extraction (FIG. 3a ). The 112 bp fragments were amplified as expected from the exosomes from the tumor serum (See Lane 4 in FIG. 3a ) and the primary tumor cells (See Lane 6 in FIG. 3a ) but not from the exosomes from normal human fibroblasts (See Lane 5 in FIG. 3a ). The 216 bp fragment could not be amplified from exosomes of all three origins. However, fragments of both 112 bp and 216 bp were amplified when the genomic DNA isolated from the glioblastoma cell was used as templates (See Lane 3 in FIG. 3a ). Thus, spliced GAPDH DNA exists within exosomes isolated from tumor cells but not within exosomes isolated from normal fibroblast cells.

In contrast, in another experiment, isolated exosomes were not treated with DNase before being lysed for DNA extraction (FIG. 3b ). Not only the 112 bp fragments but also the 216 bp fragments were amplified from exosomes isolated from primary melanoma cells (See Lane 3 in FIG. 3b ), suggesting that non-spliced GAPDH DNA or partially spliced cDNA that has been reverse transcribed exists outside of the exosomes.

For the Human Endogenous Retrovirus K (HERV-K) gene, the following primers were used: HERVK_6Forw (SEQ ID NO: 3) and HERVK_6Rev (SEQ ID NO: 4). The primer pair amplifies a 172 bp amplicon. DNA was extracted from exosomes that were isolated and treated with DNase, and used as the template for PCR amplification. As shown in FIG. 3 c, 172 bp fragments were amplified in all tumor and normal human serum exosomes but not in exosomes from normal human fibroblasts. These data suggest that unlike exosomes from normal human fibroblasts, tumor and normal human serum exosomes contain endogenous retrovirus DNA sequences. To examine if tumor exosomes also contain transposable elements, the following LINE-1 specific primers were used for PCR amplifications: Line1_Forw (SEQ ID NO: 5) and Line1_Rev (SEQ ID NO: 6). These two primers are designed to detect LINE-1 in all species since each primer contains equal amounts of two different oligos. For the Line1_Forw primer, one oligo contains a C and the other oligo contains a G at the position designated with “s”. For the Line1_Rev primer, one oligo contains an A and the other oligo contains a G at the position designated with “r”. The primer pair amplifies a 290 bp amplicon. The template was the DNA extracted from exosomes that were treated with DNase (as described above). As shown in FIG. 3 e, 290 bp LINE-1 fragments could be amplified from the exosomes from tumor cells and normal human serum but not from exosomes from the normal human fibroblasts.

To test if exosomes also contain Tenascin-C DNA, the following primer pair was used to perform PCR: Tenascin C Forw (SEQ ID NO: 7) and Tenascin C Rev (SEQ ID NO: 8). The primer pair amplifies a 197 bp amplicon. The template was the DNA extracted from exosomes that were isolated and then treated with DNase before lysis. As shown in FIG. 3 d, 197 bp Tenascin C fragments were amplified in exosomes from tumor cells or normal human serum but not in exosomes from normal human fibroblasts. Thus, Tenascin-C DNA exists in tumor and normal human serum exosomes but not in exosomes from normal human fibroblasts.

To further confirm the presence of DNA in exosomes, exosomal DNA was extracted from D425 medulloblastoma cells using the method described above. Specifically, the exosomes were isolated and treated with DNase before lysis. Equal volumes of the final DNA extract were either treated with DNase or not treated with DNase before being visualized by Ethidium Bromide staining in 1% agarose gel. Ethidium Bromide is a dye that specifically stains nucleic acids and can be visualized under ultraviolet light. As shown in FIG. 3f , Ethidium Bromide staining disappeared after DNase treatment (See Lane 3 in FIG. 3f ) while strong staining could be visualized in the un-treated aliquot (See Lane 2 in FIG. 3f ). The DNase treated and non-treated extracts were also analyzed on a RNA pico chip (Agilent Technologies). As shown in FIG. 3g , single stranded DNA could be readily detected in the DNase-non-treated extract (See upper panel in FIG. 3g ) but could barely be detected in the DNase-treated extract (See lower panel in FIG. 3g ).

To test whether the extracted DNA was single-stranded, nucleic acids were extracted from the treated exosomes as described in the previous paragraph and further treated with RNAse to eliminate any RNA contamination. The treated nucleic acids were then analyzed on a RNA pico Bioanalyzer chip and in a DNA 1000 chip. The RNA pico chip only detects single stranded nucleic acids. The DNA 1000 chip detected double stranded nucleic acids. As shown in FIG. 3h , single stranded nucleic acids were detected (See upper panel) but double stranded nucleic acids were not detected (See lower panel). Thus, the DNA contained within tumor exosomes are mostly single stranded.

To demonstrate that single stranded DNA exists in tumor cells but not in normal human fibroblasts, nucleic acids were extracted from exosomes from either glioblastoma patient serum or normal human fibroblasts. The exosomes were treated with DNase before lysis and the purified nucleic acids were treated with RNase before analysis. As shown in FIG. 3i , exosomal nucleic acids extracted from glioblastoma patient serum could be detected by a RNA pico chip. In contrast, only a very small amount of single stranded DNA was extracted from normal human fibroblasts.

Accordingly, exosomes from tumor cells and normal human serum were found to contain single-stranded DNA. The single-stranded DNA is a reverse transcription product since the amplification products do not contain introns (FIG. 3a and FIG. 3b ). It is known that tumor cells as well as normal progenitor cells/stem cells have active reverse transcriptase (RT) activity although the activity in normal progenitor cells/stem cells is relatively much lower. This RT activity makes it plausible that RNA transcripts in the cell can be reverse transcribed and packaged into exosomes as cDNA. Interestingly, exosomes from tumor cells contain more cDNAs corresponding to tumor-specific gene transcripts since tumor cells usually have up-regulated reverse transcriptase activity. Therefore, tumor specific cDNA in exosomes may be used as biomarkers for the diagnosis or prognosis of different tumor types. The use of cDNAs as biomarkers would skip the step of reverse transcription compared to the used of mRNA as biomarkers for tumors. In addition, the use of exosomal cDNA is advantageous over the use of whole serum/plasma DNA because serum/plasma contains genomic DNA released from dying cells. When testing amplified whole serum/plasma DNA, there will be more background.

Example 4: Most Extracellular RNA in Human Serum is Contained within Exosomes

To determine the amount of RNA circulating in serum as “free RNA”/RNA-protein complex versus the amount of RNA contained within the exosomes, we isolated serum from a healthy human subject, and evenly split the serum into two samples with equal volume. For sample 1, the serum was ultracentrifuged to remove most microvesicles. Then the serum supernatant was collected and RNA left in the supernatant was extracted using Trizol LS. For sample 2, the serum was not ultracentrifuged and total RNA was extracted from the serum using Trizol LS. The amount of RNA in the sample 1 supernatant and sample 2 serum was measured. As a result, it was found that the amount of free RNA in sample 1 supernatant was less than 10% of the amount of total RNA isolated from the serum sample 2. Therefore, a majority of the RNA in serum is associated with the exosomes.

Example 5: High Efficiency of Serum Extracellular Nucleic Acid Extraction is Achieved by Incorporating a Serum Exosome Isolation Step

Whole serum and plasma contain large amounts of circulating DNA and possibly also RNA protected in protein complexes, while free RNA have a half-life of a few minutes in serum. Extracellular nucleic acid profiles in serum vary between normal and diseased mammals and thus may be biomarkers for certain diseases. To examine the profiles, nucleic acids need to be extracted. However, direct extraction of nucleic acids from serum and plasma is not practical, especially from large serum/plasma volumes. In this case, large volumes of Trizol LS (a RNA extraction reagent) are used to instantly inactivate all serum nucleases before extracting the exosomal nucleic acids. Subsequently, contaminants precipitate into the sample and affect subsequent analyses. As shown in Example 4, most extracellular RNAs in serum are contained in serum exosomes. Therefore, we tested whether it is more efficient to isolate extracellular nucleic acids by isolating the serum exosomes before nucleic acid extraction.

Four milliliter (ml) blood serum from a patient was split into 2 aliquots of 2 ml each. Serum exosomes from one aliquot were isolated prior to RNA extraction. The methods of exosome isolation and RNA extraction are the same as mentioned in Example 2. For the other aliquot, RNA was extracted directly using Trizol LS according to manufacturer's recommendation. The nucleic acids from these two extractions were analyzed on a Bioanalyzer RNA chip (Agilent Technologies). As shown in FIG. 4, the amount of RNA extracted with the former method is significantly more than that obtained from the latter method. Further, the quality of RNA extracted with the latter method is relatively poor compared to that with the former method. Thus, the step of exosome isolation contributes to the efficiency of extracellular RNA extraction from serum.

Example 6: Microarray Analysis of mRNA

Microarray analysis of the mRNA population in glioblastoma cells and microvesicles derived from them was performed by Miltenyi Biotech (Auburn, Calif., USA) using the Agilent Whole Human Genome Microarray, 4×44K, two color array. The microarray analysis was performed on two different RNA preparations from primary glioblastoma cells and their corresponding microvesicles RNA preparations prepared as described in Examples 1 and 2. The data was analyzed using the GeneSifter software (Vizxlabs, Seattle, Wash., USA). The Intersector software (Vizxlabs) was used to extract the genes readily detected on both arrays. The microarray data have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO series accession number GSE13470.

We found approximately 22,000 gene transcripts in the cells and 27,000 gene transcripts in the microvesicles that were detected well above background levels (99% confidence interval) on both arrays. Approximately 4,700 different mRNAs were detected exclusively in microvesicles on both arrays, indicating a selective enrichment process within the microvesicles. Consistent with this, there was a poor overall correlation in levels of mRNAs in the microvesicles as compared to their cells of origin from two tumor cell preparations (FIGS. 2a and 2b ). In contrast, there was a good correlation in levels of mRNA from one cell culture (A) versus the second cell culture (B) (FIG. 2c ) and a similar correlation in levels of mRNA from the corresponding microvesicles (A) and (B) (FIG. 2d ). Accordingly, there is a consistency of mRNA distribution within the tumor cells and microvesicles. In comparing the ratio of transcripts in the microvesicles versus their cells of origin, we found 3,426 transcripts differentially distributed more than 5-fold (p-value <0.01). Of these, 2,238 transcripts were enriched (up to 380 fold) and 1,188 transcripts were less abundant (up to 90 fold) than in the cells (FIG. 5). The intensities and ratios of all gene transcripts were documented. The ontologies of mRNA transcripts enriched or reduced more than 10-fold were recorded and reviewed.

The mRNA transcripts that were highly enriched in the microvesicles were not always the ones that were most abundant in the microvesicles. The most abundant transcripts would be more likely to generate an effect in the recipient cell upon delivery, and therefore the 500 most abundant mRNA transcripts present in microvesicles were divided into different biological processes based on their ontology descriptions (FIG. 6a ). Of the various ontologies, angiogenesis, cell proliferation, immune response, cell migration and histone modification were selected for further study as they represent specific functions that could be involved in remodeling the tumor stroma and enhancing tumor growth. Glioblastoma microvesicle mRNAs belonging to these five ontologies were plotted to compare their levels and contribution to the mRNA spectrum (FIG. 6b ). All five ontologies contained mRNAs with very high expression levels compared to the median signal intensity level of the array.

A thorough analysis of mRNAs that are enriched in the microvesicles versus donor cells, suggests that there may be a cellular mechanism for localizing these messages into microvesicles, possibly via a “zip code” in the 3′UTR as described for mRNAs translated in specific cellular locations, such as that for beta actin (Kislauskis et al., 1994). The conformation of the mRNAs in the microvesicles is not known, but they may be present as ribonuclear particles (RNPs) (Mallardo et al., 2003) which would then prevent degradation and premature translation in the donor cell.

Microarray analysis of the mRNA populations in glioblastoma cells and microvesicles derived from glioblastoma cells, melanoma cells, and microvesicles derived from melanoma cells was performed by Illumina Inc. (San Diego, Calif., USA) using the Whole-Genome cDNA-mediated Annealing, Selection, Extension, and Ligation (DASL) Assay. The Whole-Genome DASL Assay combines the PCR and labeling steps of Illumina's DASL Assay with the gene-based hybridization and whole-genome probe set of Illumina's HumanRef-8 BeadChip. This BeadChip covers more than 24,000 annotated genes derived from RefSeq (Build 36.2, Release 22). The microarray analysis was performed on two different RNA preparations from primary glioblastoma cells, microvesicles from glioblastomas cells (derived with the method as described in Examples 1 and 2), melanoma cells, and microvesicles from melanoma cells (derived with the method as described in Examples 1 and 2).

The expression data for each RNA preparation were pooled together and used to generate a cluster diagram. As shown in FIG. 7, mRNA expression profiles for glioblastoma cells, microvesicles from glioblastomas cells, melanoma cells, and microvesicles from melanoma cells are clustered together, respectively. Expression profiles of the two primary glioblastoma cell lines 20/3C and 11/5c are clustered with a distance of about 0.06. Expression profiles of the two primary melanoma cell lines 0105C and 0664C are clustered with a distance of about 0.09. Expression profiles of exosomes from the two primary melanoma cell lines 0105C and 0664C are clustered together with a distance of around 0.15. Expression profiles of exosomes from the two primary glioblastomas cell lines 20/3C and 11/5c are clustered together with a distance of around 0.098. Thus, exosomes from glioblastoma and melanoma have distinctive mRNA expression signatures and the gene expression signature of exosomes differs from that of their original cells. These data demonstrate that mRNA expression profiles from microvesicles may be used in the methods described herein for the diagnosis and prognosis of cancers.

Example 7: Glioblastoma Microvesicles Contain miRNA

Mature miRNA from microvesicles and from donor cells was detected using a quantitative miRNA reverse transcription PCR. Specifically, total RNA was isolated from microvesicles and from donor cells using the mirVana RNA isolation kit (Applied Biosystems, Foster City, Calif., USA). Using the TaqMan® MicroRNA Assay kits (Applied Biosystems, Foster City, Calif., USA), 30 ng total RNA was converted into cDNA using specific miR-primers and further amplified according to the manufacturer's protocol.

A subset of 11 miRNAs among those known to be up-regulated and abundant in gliomas was analyzed in microvesicles purified from two different primary glioblastomas (GBM 1 and GBM 2). These subset contained let-7a, miR-15b, miR-16, miR-19b, miR-21, miR-26a, miR-27a, miR-92, miR-93, miR-320 and miR-20. All of these miRNA were readily detected in donor cells and in microvesicles (FIG. 8). The levels were generally lower in microvesicles per μg total RNA than in parental cells (10%, corresponding to approximately 3 Ct-values), but the levels were well correlated, indicating that these 11 miRNA species are not enriched in microvesicles.

Microarray analysis of the microRNA populations in glioblastoma cells and microvesicles derived from glioblastoma cells, melanoma cells, and microvesicles derived from melanoma cells was performed by Illumina Inc. (San Diego, Calif., USA) using the MicroRNA Expression Profiling Panel, powered by the DASL Assay. The human MicroRNA Panels include 1146 microRNA species. The microarray analysis was performed on two different RNA preparations from primary glioblastoma cells, microvesicles from glioblastomas cells (derived using the method described in Examples 1 and 2), melanoma cells, and microvesicles from melanoma cells (derived using the method described in Examples 1 and 2).

The expression data for each RNA preparation were pooled together and used to generate a cluster diagram. As shown in FIG. 9, microRNA expression profiles for glioblastoma cells, microvesicles from glioblastomas cells, melanoma cells, and microvesicles from melanoma cells are clustered together, respectively. Expression profiles of the two primary melanoma cell lines 0105C and 0664C are clustered with a distance of about 0.13. Expression profiles of the two primary glioblastomas cell lines 20/3C and 11/5c are clustered with a distance of about 0.12. Expression profiles of exosomes from the two primary glioblastomas cell lines 20/3C and 11/5c are clustered together with a distance of around 0.12. Expression profiles of exosomes from the two primary melanoma cell lines 0105C and 0664C are clustered together with a distance of around 0.17. Thus, exosomes from glioblastoma and melanoma have distinctive microRNA expression signatures and that the gene expression signature of exosomes differs from that of their original cells. Furthermore, as demonstrated herein, microRNA expression profiles from microvesicles may be used in the methods described herein for the diagnosis and prognosis of cancers.

The finding of miRNAs in microvesicles suggests that tumor-derived microvesicles can modify the surrounding normal cells by changing their transcriptional/translational profiles. Furthermore, as demonstrated herein, miRNA expression profile from microvesicles may be used in the methods described herein for the diagnosis and prognosis of cancers, including but not limited to glioblastoma.

Examples 8-15. These Examples Show that Nucleic Acids within Exosomes from Bodily Fluids can be Used as Biomarkers for Diseases or Other Medical Conditions Example 8: Expression Profiles of miRNAs in Microvesicles can be Used as Sensitive Biomarkers for Glioblastoma

To determine if microRNAs within exosomes may be used as biomarkers for a disease and/or medical condition, we examined the existence of a correlation between the expression level of microRNA and disease status. Since microRNA-21 is expressed at high levels in glioblastoma cells and is readily detectable in exosomes isolated from serum of glioblastoma patients, we measured quantitatively microRNA-21 copy numbers within exosomes from the sera of glioblastoma patients by quantitative RT-PCR. Specifically, exosomes were isolated from 4 ml serum samples from 9 normal human subjects and 9 glioblastoma patients. The RNA extraction procedure was similar to the RNA extraction procedure as described in Example 2. The level of miR-21 was analyzed using singleplex qPCR (Applied Biosystems) and normalized to GAPDH expression level.

As shown in FIG. 10, the average Ct-value was 5.98 lower in the glioblastoma serum sample, suggesting that the exosomal miRNA-21 expression level in glioblastoma patients is approximately 63 fold higher than that in a normal human subject. The difference is statistically significant with a p value of 0.01. Therefore, there is a correlation between microRNA-21 expression level and glioblastoma disease status, which demonstrates that validity and applicability of the non-invasive diagnostic methods disclosed herein. For example, in one aspect, the method comprised the steps of isolating exosomes from the bodily fluid of a subject and analyzing microRNA-21 expression levels within the exosomes by measuring the copy number of microRNA-21 and comparing the number to that within exosomes from a normal subject or to a standard number generated by analyzing micro-RNA-21 contents within exosomes from a group of normal subjects. An increased copy number indicates the existence of glioblastoma in the subject; while the absence of an increased copy number indicates the absence of glioblastoma in the subject. This basic method may be extrapolated to diagnose/monitor other diseases and/or medical conditions associated with other species of microRNAs.

Example 9: mRNAs in Microvesicles can be Used as Sensitive Biomarkers for Diagnosis

Nucleic acids are of high value as biomarkers because of their ability to be detected with high sensitivity by PCR methods. Accordingly, the following tests were designed and carried out to determine whether the mRNA in microvesicles could be used as biomarkers for a medical disease or condition, in this case glioblastoma tumors. The epidermal growth factor receptor (EGFR) mRNA was selected because the expression of the EGFRvIII mutation is specific to some tumors and defines a clinically distinct subtype of glioma (Pelloski et al., 2007). In addition, EGFRvIII mutations traditionally cannot be detected using tissues other than the lesion tissues since these mutations are somatic mutations but not germ line mutations. Therefore, a biopsy from lesion tissues such as glioma tumor is conventionally required for detecting EGFRvIII mutations. As detailed below, nested RT-PCR was used to identify EGFRvIII mRNA in glioma tumor biopsy samples and the results compared with the mRNA species found in microvesicles purified from a serum sample from the same patient.

Microvesicles were purified from primary human glioblastoma cells followed by RNA extraction from both the microvesicles and donor cells (biopsy). The samples were coded and the PCRs were performed in a blind fashion. Gli-36EGFRvIII (human glioma cell stably expressing EGFRvIII) was included as a positive control. The microvesicles from 0.5-2 ml of frozen serum samples were pelleted as described in Example 2 and the RNA was extracted using the MirVana Microvesicles RNA isolation kit. Nested RT-PCR was then used to amplify both the wild type EGFR (1153 bp) and EGFRvIII (352 bp) transcripts from both the microvesicles and donor cells using the same set of primers. Specifically, the RNA was converted to cDNA using the Omniscript RT kit (Qiagen Inc, Valencia, Calif., USA) according to the manufacturer's recommended protocol. GAPDH primers were GAPDH Forward (SEQ ID NO: 9) and GAPDH Reverse (SEQ ID NO: 10). The EGFR/EGFRvIII PCR1 primers were SEQ ID NO: 11 and SEQ ID NO: 12. The EGFR/EGFRvIII PCR2 primers were SEQ ID NO: 13 and SEQ ID NO: 14. The PCR cycling protocol was 94° C. for 3 minutes; 94° C. for 45 seconds, 60° C. for 45 seconds, 72° C. for 2 minutes for 35 cycles; and a final step 72° C. for 7 minutes.

We analyzed the biopsy sample to determine whether the EGFRvIII mRNA was present and compared the result with RNA extracted from exosomes purified from a frozen serum sample from the same patient. Fourteen of the 30 tumor samples (47%) contained the EGFRvIII transcript, which is consistent with the percentage of glioblastomas found to contain this mutation in other studies (Nishikawa et al., 2004). EGFRvIII could be amplified from exosomes in seven of the 25 patients (28%) from whom serum was drawn around the time of surgery (FIG. 11 and Table 1). When a new pair of primers EGFR/EGFRvIII PCR3: SEQ ID NO: 15 and SEQ ID NO: 16, were used as the second primer pair for the above nested PCR amplification, more individuals were found to harbor EGFRvIII mutations (Table 1). EGFRvIII could be amplified from exosomes in the six patients who was identified as negatives with the old pair of primers EGFRvIII PCR2: SEQ ID NO: 13 AND SEQ ID NO: 14. Notably, exosomes from individual 13, whose biopsy did not show EGFRvIII mutation, was shown to contain EGFRvIII mutation, suggesting an increased sensivity of EGFRvIII mutation detection using exosomes technology. From the exosomes isolated from 52 normal control serum samples, EGFRvIII could not be amplified (FIG. 12). Interestingly, two patients with an EGFRvIII negative tumor sample turned out to be EGFRvIII positive in the serum exosomes, supporting heterogeneous foci of EGFRvIII expression in the glioma tumor. Furthermore, our data also showed that intact RNAs in microvesicles were, unexpectedly, able to be isolated from frozen bodily serum of glioblastoma patients. These blind serum samples from confirmed glioblastoma patients were obtained from the Cancer Research Center (VU medical center, Amsterdam, the Netherlands) and were kept at −80° C. until use. The identification of tumor specific RNAs in serum microvesicles allows the detection of somatic mutations which are present in the tumor cells. Such technology should result in improved diagnosis and therapeutic decisions.

The RNA found in the microvesicles contains a “snapshot” of a substantial array of the cellular gene expression profile at a given time. Among the mRNA found in glioblastoma-derived microvesicles, the EGFR mRNA is of special interest since the EGFRvIII splice variant is specifically associated with glioblastomas (Nishikawa et al., 2004). Here it is demonstrated that brain tumors release microvesicles into the bloodstream across the blood-brain-barrier (BBB), which has not been shown before. It is further demonstrated that mRNA variants, such as EGFRvIII in brain tumors, are able to be detected by a method comprising the steps of isolating exosomes from a small amount of patient serum and analyzing the RNA in said microvesicles.

Knowledge of the EGFRvIII mutation in tumors is important in choosing an optimal treatment regimen. EGFRvIII-positive gliomas are over 50 times more likely to respond to treatment with EGFR-inhibitors like erlotinib or gefitinib (Mellinghoff et al., 2005).

Example 10: Diagnosis of Iron Metabolism Disorders

The exosome diagnostics method can be adapted for other purposes as shown by the following example.

Hepcidin, an antimicrobial peptide, is the master hormonal regulator of iron metabolism. This peptide is produced mainly in mammalian liver and is controlled by the erythropoietic activity of the bone-marrow, the amount of circulating and stored body iron, and inflammation. Upon stimulation, hepcidin is secreted into the circulation or urine where it may act on target ferroportin-expressing cells. Ferroportin is the sole iron exporter identified to date and when bound to hepcidin, it is internalized and degraded. The resulting destruction of ferroportin leads to iron retention in ferroportin expressing cells such as macrophages and enterocytes. This pathophysiological mechanism underlies anemia of chronic diseases. More specifically, inappropriately high levels of hepcidin and elevated iron content within the reticuloendothelial system characterize anemia. Indeed, anemia may be associated with many diseases and/or medical conditions such as infections (acute and chronic), cancer, autoimmune, chronic rejection after solid-organ transplantation, and chronic kidney disease and inflammation (Weiss and Goodnough, 2005). On the other hand, in a genetic iron overload disease such as hereditary hemochromatosis, inappropriately low expression levels of hepcidin encourage a potentially fatal excessive efflux of iron from within the reticuloendothelial system. So, hepcidin is up-regulated in anemia associated with chronic disease, but down-regulated in hemochromatosis.

Currently, there is no suitable assay to quantitatively measure hepcidin levels in circulation or urine (Kemna et al., 2008) except time-of-flight mass spectrometry (TOF MS), which needs highly specialized equipment, and therefore is not readily accessible. Recently, the method of Enzyme Linked ImmunoSorbent Assay (ELISA) has been proposed to quantitatively measure hepcidin hormone levels but this method is not consistent because of the lack of clear correlations with hepcidin (Kemna et al., 2005; Kemna et al., 2007) and other iron related parameters (Brookes et al., 2005; Roe et al., 2007).

Hepcidin mRNA was detected in exosomes from human serum, as follows.

Exosomes were first isolated from human serum and their mRNA contents extracted before conversion to cDNA and PCR amplification. PCR primers were designed to amplify a 129 nucleotide fragment of human Hepcidin. The sequences of the primers are SEQ ID NO: 57 and SEQ ID NO: 58. A hepcidin transcript of 129 nucleotides (the middle peak in FIG. 13D) was readily detected by Bioanalyzer. As a positive control (FIG. 13B), RNA from a human hepatoma cell line Huh-7 was extracted and converted to cDNA. The negative control (FIG. 13C) is without mRNA. These Bioanalyzer data are also shown in the pseudogel in FIG. 13A.

Hepcidin mRNA in microvesicles in circulation correlates with hepcidin mRNA in liver cells. Hence, measuring hepcidin mRNA within microvesicles in a bodily fluid sample would allow one to diagnose or monitor anemia or hemochromatosis in the subject.

Thus, it is possible to diagnose and/or monitor anemia and hemochromatosis in a subject by isolating microvesicles from a bodily fluid and comparing the hepcidin mRNA in said microvesicles with the mRNA from a normal subject. With an anemic subject, the copy number of mRNA is increased over the normal, non-anemic level. In a subject suffering from hemochromatosis, the copy number is decreased relative to the mRNA in a normal subject.

Example 11: Non-Invasive Transcriptional Profiling of Exosomes for Diabetic Nephropathy Diagnosis

Diabetic nephropathy (DN) is a life threatening complication that currently lacks specific treatments. Thus, there is a need to develop sensitive diagnostics to identify patients developing or at risk of developing DN, enabling early intervention and monitoring.

Urine analysis provides a way to examine kidney function without having to take a biopsy. To date, this analysis has been limited to the study of protein in the urine. This Example sets forth a method to obtain from urine transcriptional profiles derived from cells that normally could only be obtained by kidney biopsy. Specifically, the method comprises the steps of isolating urine exosomes and analyzing the RNAs within said exosomes to obtain transcriptional profiles, which can be used to examine molecular changes being made by kidney cells in diabetic individuals and provide a ‘snap shot’ of any new proteins being made by the kidney. State-of-the-art technologies to obtain exosomal transcription profiles include, but are not limited to, contemporary hybridization arrays, PCR based technologies, and next generation sequencing methods. Since direct sequencing does not require pre-designed primers or spotted DNA oligos, it will provide a non-biased description of exosomal RNA profiles. An example of next generation sequencing technology is provided by the Illumina Genome Analyzer, which utilizes massively parallel sequencing technology which allows it to sequence the equivalent of ⅓ a human genome per run. The data obtainable from this analysis would enable one to rapidly and comprehensively examine the urinary exosomal transcriptional profile and allow comparison to the whole kidney. Using such a method, one could obtain much needed information regarding the transcription profile of urinary exosomes. A comparison of transcripts in control versus diabetes-derived urinary exosomes could further provide one with a comprehensive list of both predicted and new biomarkers for diabetic nephropathy.

In order to prove the feasibility of the diagnostic method described above, an experiment was designed and carried out to isolate urinary exosomes and to confirm the presence of renal specific biomarkers within these exosomes. In this experiment, a fresh morning urine sample of 220 ml was collected from a 28-year old healthy male subject and processed via differential centrifugation to isolate urinary exosomes. Specifically, urine was first spun at 300×g spin for 10 minutes to remove any cells from the sample. The supernatant was collected and then underwent a 20-minute 16,500×g spin to bring down any cell debris or protein aggregates. The supernatant was then passed through a 0.22 uM membrane filter to remove debris with diameters larger than 0.22 uM. Finally, the sample underwent ultra-centrifugation at 100,000×g for 1 hour to pellet the exosomes (Thery et al., 2006). The pellet was gently washed in phosphate buffered saline (PBS) and RNA was extracted using a Qiagen RNeasy kit pursuant to the manufacturer's instructions. The isolated RNA was converted to cDNA using the Omniscript RT kit (Qiagen) followed by PCR amplification of renal specific genes.

The renal specific genes examined and their corresponding renal area where the gene is expressed are as follows: AQP1—proximal tubules; AQP2—distal tubule (principal cells); CUBN—proximal tubules; LRP2—proximal tubules; AVPR2—proximal and distal tubules; SLC9A3 (NHE-3)—Proximal tubule; ATP6V1B1—distal tubule (intercalated cells); NPHS1—glomerulus (podocyte cells); NPHS2—glomerulus (podocyte cells); and CLCN3—Type B intercalated cells of collecting ducts. The sequences of the primers designed to amplify each gene are AQP1-F (SEQ ID NO: 17) and AQP1-R (SEQ ID NO: 18); AQP2-F (SEQ ID NO: 19) and AQP2-R (SEQ ID NO: 20); CUBN-F (SEQ ID NO: 21) and CUBN-R (SEQ ID NO: 22); LRP2-F (SEQ ID NO: 23) and LRP2-R (SEQ ID NO: 24); AVPR2-F (SEQ ID NO: 25) and AVPR2-R (SEQ ID NO: 26); SLC9A3-F (SEQ ID NO: 27) and SLC9A3-R (SEQ ID NO: 28); ATP6V1B1-F (SEQ ID NO: 29) and ATP6V1B1-R (SEQ ID NO: 30); NPHS1-F (SEQ ID NO: 31) and NPHS1-R (SEQ ID NO: 32); NPHS2-F (SEQ ID NO: 33) and NPHS2-R (SEQ ID NO: 34); CLCN5-F (SEQ ID NO: 35) and CLCN5-R (SEQ ID NO: 36).

The expected sizes of the PCR products for each gene are AQP1-226 bp, AQP2-208 bp, CUBN-285 bp, LRP2-220 bp, AVPR2-290 bp, SLC9A3-200 bp, ATP6V1B1-226 bp, NPHS1-201 bp, NPHS2-266 bp and CLCN5-204 bp. The PCR cycling protocol was 95° C. for 8 minutes; 95° C. for 30 seconds, 60° C. for 30 seconds, 72° C. for 45 seconds for 30 cycles; and a final step 72° C. for 10 minutes.

As shown in FIG. 14a , kidney tubule cells contain multivesicular bodies, which is an intermediate step during exosome generation. Exosomes isolated from these cells can be identified by electron microscopy (FIG. 14b ). Analysis of total RNA extracted from urinary exosomes indicates the presence of RNA species with a broad range of sizes (FIG. 14c ). 18S and 28S ribosomal RNAs were not found. PCR analysis confirmed the presence of renal specific transcripts within urinary exosomes (FIG. 14d ). These data show that kidney cells shed exosomes into urine and these urinary exosomes contain transcripts of renal origin, and that the exosome method can detect renal biomarkers associated with certain renal diseases and/or other medical conditions.

To further confirm the presence of renal specific mRNA transcripts in urinary exosomes, an independent set of experiments were performed using urine samples from six individuals. Exosomal nucleic acids were extracted from 200 ml morning urine samples from each individual following a procedure as mentioned above. Specifically, urine samples underwent differential centrifugation starting with a 1000×g centrifugation to spin down whole cells and cell debris. The supernatant was carefully removed and centrifuged at 16,500×g for 20 minutes. The follow-on supernatant was then removed and filtered through a 0.8 μm filter to remove residual debris from the exosome containing supernatant. The final supernatant then underwent ultracentrifugation at 100,000×g for 1 hr 10 min. The pellet was washed in nuclease free PBS and re-centrifuged at 100,000×g for 1 hr 10 min to obtain the exosomes pellet which is ready for nucleic acid extraction. Nucleic acids were extracted from the pelleted exosomes using the Arcturus PicoPure RNA Isolation kit and the nucleic acid concentration and integrity was analyzed using a Bioanalyzer (Agilent) Pico chip. As shown in FIG. 14e , nucleic acids isolated from urinary exosomes vary from individual to individual. To test whether the presence of renal biomarkers also varies from individual to individual, PCR amplifications were carried out for Aquaporin1, Aquaporin2 and Cubilin gene using a new set of primer pairs: AQP1 new primer pair: SEQ ID NO: 37 and SEQ ID NO: 38; AQP2 new primer pair: SEQ ID NO: 39 and SEQ ID NO: 40; CUBN new primer pair: SEQ ID NO: 41 and SEQ ID NO: 42. These primer pairs were designed specifically to amplify the spliced and reverse transcribed cDNA fragments. Reverse transcription was performed using the Qiagen Sensiscript kit. As shown in FIG. 14f , no amplification was seen in individual 1, probably due to failed nucleic acid extraction. AQP1 was amplified only in individual 2. CUBN was amplified in individual 2 and 3. And AQP2 was amplified in individual 2, 3, 4 and 5. In comparison actin gene (indicated by “House” in FIG. 14f ) was amplified in individual 2, 3, 4, 5 and 6. These data provide more evidence that urinary exosomes contain renal specific mRNA transcripts although the expression levels are different between different individuals.

To test the presence of cDNAs in urinary exosomes, a 200 ml human urine sample was split into two 100 ml urine samples. Urinary exosomes were isolated from each sample. Exosomes from one sample were treated with DNase and those from the other sample were mock treated. Exosomes from each sample were then lysed for nucleic acid extraction using PicoPure RNA isolation kit (Acturus). The nucleic acids were used as templates for nested-PCR amplification (PCR protocols described in Example 9) without prior reverse transcription. The primer pairs to amplify the actin gene were Actin-FOR (SEQ ID NO: 43) and Actin-REV (SEQ ID NO: 44); Actin-nest-FOR (SEQ ID NO: 45) and Actin-nest-REV (SEQ ID NO: 46) with an expected final amplicon of 100 bp based on the actin gene cDNA sequence. As shown in FIG. 14g , the 100 bp fragments were present in the positive control (human kidney cDNA as templates), DNase treated and non-treated exosomes, but absent in the negative control lane (without templates). Accordingly, actin cDNA is present in both the DNase treated and non-treated urinary exosomes.

To test whether most nucleic acids extracted using the method were present within exosomes, the nucleic acids extracted from the DNase treated and non-treated exosomes were dissolved in equal volumes and analyzed using a RNA Pico chip (Agilent Technologies). As shown in FIG. 14h , the concentration of the isolated nucleic acids from the DNase treated sample was 1,131 pg/ul and that from the non-treated sample was 1,378 pg/ul. Thus, more than 80% nucleic acids extracted from urinary exosomes using the above method were from inside exosomes.

To identify the content of urinary exosomes systematically, nucleic acids were extracted from urinary exosomes and submitted to the Broad Institute for sequencing. Approximately 14 million sequence reads were generated, each 76 nucleotides in length. These sequence reads correspond to fragments of DNA/RNA transcripts present within urinary exosomes. Using an extremely strict alignment parameter (100% identity over full length sequence), approximately 15% of the reads were aligned to the human genome. This percentage would likely increase if less stringent alignment criteria was used. A majority of these 15% reads did not align with protein coding genes but rather with non-coding genomic elements such are transposons and various LINE & SINE repeat elements. Notably, for those reads that are not aligned to the human genome, many are aligned to viral sequences. To the extent that the compositions and levels of nucleic acids contained in urinary exosomes change with respect to a disease status, profiles of the nucleic acids could be used according to the present methods as biomarkers for disease diagnosis.

This example demonstrates that the exosome method of analyzing urine exosomes can be used to determine cellular changes in the kidney in diabetes-related kidney disease without having to take a high-risk, invasive renal biopsy. The method provides a new and sensitive diagnostic tool using exosomes for early detection of kidney diseases such as diabetic nephropathy. This will allow immediate intervention and treatment. In sum, the exosome diagnostic method and technology described herein provides a means of much-needed diagnostics for diabetic nephropathy and other diseases which are associated with certain profiles of nucleic acids contained in urinary exosomes.

Example 12: Prostate Cancer Diagnosis and Urinary Exosomes

Prostate cancer is the most common cancer in men today. The risk of prostate cancer is approximately 16%. More than 218,000 men in the United States were diagnosed in 2008. The earlier prostate cancer is detected, the greater are the chances of successful treatment. According to the American Cancer Society, if prostate cancers are found while they are still in the prostate itself or nearby areas, the five-year relative survival rate is over 98%.

One established diagnostic method is carried out by measuring the level of prostate specific antigen (PSA) in the blood, combined with a digital rectal examination. However, both the sensitivity and specificity of the PSA test requires significant improvement. This low specificity results in a high number of false positives, which generate numerous unnecessary and expensive biopsies. Other diagnostic methods are carried out by detecting the genetic profiles of newly identified biomarkers including, but not limited to, prostate cancer gene 3 (PCA3) (Groskopf et al., 2006; Nakanishi et al., 2008), a fusion gene between transmembrane protease serine 2 and ETS-related gene (TMPRSS2-ERG) (Tomlins et al., 2005), glutathione S-transferase pi (Goessl et al., 2000; Gonzalgo et al., 2004), and alpha-methylacyl CoA racemase (AMACR) (Zehentner et al., 2006; Zielie et al., 2004) in prostate cancer cells found in bodily fluids such as serum and urine (Groskopf et al., 2006; Wright and Lange, 2007). Although these biomarkers may give increased specificity due to overexpression in prostate cancer cells (e.g., PCA3 expression is increased 60- to 100-fold in prostate cancer cells), a digital rectal examination is required to milk prostate cells into the urine just before specimen collection (Nakanishi et al., 2008). Such rectal examinations have inherent disadvantages such as the bias on collecting those cancer cells that are easily milked into urine and the involvement of medical doctors which is costly and time consuming.

Here, a new method of detecting the genetic profiles of these biomarkers is proposed to overcome the limitation mentioned above. The method comprises the steps of isolating exosomes from a bodily fluid and analyzing the nucleic acid from said exosomes. The procedures of the method are similar to those detailed in Example 9. In this example, the urine samples were from four diagnosed prostate cancer patients. As shown in FIG. 15c , the cancer stages were characterized in terms of grade, Gleason stage and PSA levels. In addition, the nucleic acids analyzed by nested-RT-PCR as detailed in Example 7 were TMPRSS2-ERG and PCA3, two of the newly identified biomarkers of prostate cancer. For amplification of TMPRSS2-ERG, the primer pair for the first amplification step was TMPRSS2-ERG F1 (SEQ ID NO: 47) and TMPRSS2-ERG R1 (SEQ ID NO: 48); and the primer pair for the second amplification step was TMPRSS2-ERG F2 (SEQ ID NO: 49) and TMPRSS2-ERG R2 (SEQ ID NO: 50). The expected amplicon is 122 base pairs (bp) and gives two fragments (one is 68 bp, the other is 54 bp) after digestion with the restriction enzyme HaeII. For amplification of PCA3, the primer pair for the first amplification step was PCA3 F1 (SEQ ID NO: 51) and PCA3 R1 (SEQ ID NO: 52); and the primer pair for the second amplification step was PCA3 F2 (SEQ ID NO: 53) and PCA3 R2 (SEQ ID NO: 54). The expected amplicon is 152 bp in length and gives two fragments (one is 90 bp, the other is 62 bp) after digestion with the restriction enzyme Sca1.

As shown in FIG. 15a , in both patient 1 and 2, but not in patient 3 and 4, the expected amplicon of TMPRSS2-ERG could be detected and digested into two fragments of expected sizes. As shown in FIG. 15b , in all four patients, the expected amplicon of PCA3 could be detected and digested into two fragments of expected sizes. Therefore, PCA3 expression could be detected in urine samples from all four patients, while TMPRSS2-ERG expression could only be detected in urine samples from patient 1 and 2 (FIG. 15c ). These data, although not conclusive due to the small sample size, demonstrate the applicability of the new method in detecting biomarkers of prostate cancer. Further, the exosome method is not limited to diagnosis but can be employed for prognosis and/or monitoring other medical conditions related to prostate cancer.

Example 13: Microvesicles in Non-Invasive Prenatal Diagnosis

Prenatal diagnosis is now part of established obstetric practice all over the world. Conventional methods of obtaining fetal tissues for genetic analysis includes amniocentesis and chorionic villus sampling, both of which are invasive and confer risk to the unborn fetus. There is a long-felt need in clinical genetics to develop methods of non-invasive diagnosis. One approach that has been investigated extensively is based on the discovery of circulating fetal cells in maternal plasma. However, there are a number of barriers that hinder its application in clinical settings. Such barriers include the scarcity of fetal cells (only 1.2 cells/ml maternal blood), which requires relatively large volume blood samples, and the long half life of residual fetal cells from previous pregnancy, which may cause false positives. Another approach is based on the discovery of fetal DNA in maternal plasma. Sufficient fetal DNA amounts and short clearance time overcome the barriers associated with the fetal cell method. Nevertheless, DNA only confers inheritable genetic and some epigenetic information, both of which may not represent the dynamic gene expression profiles that are linked to fetal medical conditions. The discovery of circulating fetal RNA in maternal plasma (Ng et al., 2003b; Wong et al., 2005) may be the method of choice for non-invasive prenatal diagnosis.

Several studies suggest that fetal RNAs are of high diagnostic value. For example, elevated expression of fetal corticotropin-releasing hormone (CRH) transcript is associated with pre-eclampsia (a clinical condition manifested by hypertension, edema and proteinuria) during pregnancy (Ng et al., 2003a). In addition, the placenta-specific 4 (PLAC4) mRNA in maternal plasma was successfully used in a non-invasive test for aneuploid pregnancy (such as trisomy 21, Down syndrome) (Lo et al., 2007). Furthermore, fetal human chorionic gonadotropin (hCG) transcript in maternal plasma may be a marker of gestational trophoblastic diseases (GTDs), which is a tumorous growth of fetal tissues in a maternal host. Circulating fetal RNAs are mainly of placenta origin (Ng et al., 2003b). These fetal RNAs can be detected as early as the 4th week of gestation and such RNA is cleared rapidly postpartum.

Prenatal diagnosis using circulating fetal RNAs in maternal plasma, nevertheless, has several limitations. The first limitation is that circulating fetal RNA is mixed with circulating maternal RNA and is not effectively separable. Currently, fetal transcripts are identified, based on an assumption, as those that are detected in pregnant women antepartum as well as in their infant's cord blood, yet are significantly reduced or absent in maternal blood within 24 or 36 hours postpartum (Maron et al., 2007). The second limitation is that no method is established to enrich the circulating fetal RNA for enhanced diagnostic sensitivity since it is still unknown how fetal RNA is packaged and released. The way to overcome these limitations may lie in the isolation of microvesicles and the analysis of the fetal RNAs therein.

Several facts suggest that microvesicles, which are shed by eukaryotic cells, are the vehicles for circulating fetal RNAs in maternal plasma. First, circulating RNAs within microvesicles are protected from RNase degradation. Second, circulating fetal RNAs have been shown to remain in the non-cellular fraction of maternal plasma, which is consistent with the notion that microvesicles encompassing these fetal RNAs are able to be filtered through 0.22 um membrane. Third, similar to tumorous tissues which are know to shed microvesicles, placental cells, which are a pseudo-malignant fetal tissue, are most likely capable of shedding microvesicles. Thus, a novel method of non-invasive prenatal diagnosis is comprised of isolating fetal microvesicles from maternal blood plasma and then analyzing the nucleic acids within the microvesicles for any genetic variants associated with certain diseases and/or other medical conditions.

A hypothetical case of non-invasive prenatal diagnosis is as follows: peripheral blood samples are collected from pregnant women and undergo magnetic activated cell sorting (MACS) or other affinity purification to isolate and enrich fetus-specific microvesicles. The microvesicular pellet is resuspended in PBS and used immediately or stored at −20° C. for further processing. RNA is extracted from the isolated microvesicles using the Qiagen RNA extraction kit as per the manufacturer's instructions. RNA content is analyzed for the expression level of fetal human chorionic gonadotropin (hCG) transcript. An increased expression level of hCG compared to the standard range points to the development of gestational trophoblastic diseases (GTDs) and entail further the need for clinical treatment for this abnormal growth in the fetus. The sensitivity of microvesicle technology makes it possible to detect the GTDs at a very early stage before any symptomatic manifestation or structural changes become detectable under ultrasonic examination. The standard range of hCG transcript levels may be determined by examining a statistically significant number of circulating fetal RNA samples from normal pregnancies.

This prenatal diagnostic method may be extrapolated to the prenatal diagnosis and/or monitoring of other diseases or medical conditions by examining those transcripts associated with these diseases or medical conditions. For example, extraction and analysis of anaplastic lymphoma kinase (ALK) nucleic acid from microvesicles of fetus origin from maternal blood is a non-invasive prenatal diagnosis of neuroblastoma, which is closely associated with mutations within the kinase domain or elevated expression of ALK (Mosse et al., 2008). Accordingly, the microvesicle methods and technology described herein may lead to a new era of much-needed, non-invasive prenatal genetic diagnosis.

Example 14: Melanoma Diagnosis

Melanoma is a malignant tumor of melanocytes (pigment cells) and is found predominantly in skin. It is a serious form of skin cancer and accounts for 75 percent of all deaths associated with skin cancer. Somatic activating mutations (e.g. V600E) of BRAF are the earliest and most common genetic abnormality detected in the genesis of human melanoma. Activated BRAF promotes melanoma cell cycle progression and/or survival.

Currently, the diagnosis of melanoma is made on the basis of physical examination and excisional biopsy. However, a biopsy can sample only a limited number of foci within the lesion and may give false positives or false negatives. The exosome method provides a more accurate means for diagnosing melanoma. As discussed above, the method is comprised of the steps of isolating exosomes from a bodily fluid of a subject and analyzing the nucleic acid from said exosomes.

To determine whether exosomes shed by melanoma cells contain BRAF mRNA, we cultured primary melanoma cells in DMEM media supplemented with exosome-depleted FBS and harvested the exosomes in the media using a similar procedure as detailed in Example 2. The primary cell lines were Yumel and M34. The Yumel cells do not have the V600E mutation in BRAF, while M34 cells have the V600E mutation in BRAF. RNAs were extracted from the exosomes and then analyzed for the presence of BRAF mRNA by RT-PCR. The primers used for PCR amplification were: BRAF forward (SEQ ID NO: 55) and BRAF reverse (SEQ ID NO: 56). The amplicon is 118 base pairs (bp) long and covers the part of BRAF cDNA sequence where the V600E mutation is located. As shown in FIG. 16a , a band of 118 bp was detected in exosomes from primary melanoma cells (Yumel and M34 cells), but not in exosomes from human fibroblast cells or negative controls. The negative detection of a band of 118 bp PCR product is not due to a mistaken RNA extraction since GAPDH transcripts could be detected in exosomes from both melanoma cell and human fibroblast cells (FIG. 16b ). The 118 bp PCR products were further sequenced to detect the V600E mutation. As shown in FIGS. 16c and 16d , PCR products from YUMEL cells, as expected, contain wild type BRAF mRNA. In contrast, PCR products from M34 cells, as expected, contain mutant BRAF mRNA with a T-A point mutation, which causes the amino acid Valine (V) to be replaced by Glutamic acid (E) at the amino acid position 600 of the BRAF protein. Furthermore, BRAF mRNA cannot be detected in exosomes from normal human fibroblast cells, suggesting the BRAF mRNA is not contained in exosomes of all tissue origins.

These data suggest that melanoma cells shed exosomes into the blood circulation and thus melanoma can be diagnosed by isolating these exosomes from blood serum and analyzing the nucleic acid therefrom for the presence or absence of mutations (e.g., V600E) in BRAF. The method described above can also be employed to diagnose melanomas that are associated with other BRAF mutations and mutations in other genes. The method can also be employed to diagnose melanomas that are associated with the expression profiles of BRAF and other nucleic acids.

Example 15: Detection of MMP Levels from Exosomes to Monitor Post Transplantation Conditions

Organ transplants are usually effective treatments for organ failures. Kidney failure, heart disease, end-stage lung disease and cirrhosis of the liver are all conditions that can be effectively treated by a transplant. However, organ rejections caused by post-transplantation complications are major obstacles for long-term survival of the allograft recipients. For example, in lung transplantations, bronchiolitis obliterans syndrome is a severe complication affecting survival rates. In kidney transplants, chronic allograft nephropathy remains one of the major causes of renal allograft failure. Ischemia-reperfusion injury damages the donor heart after heart transplantation, as well as the donor liver after orthotopic liver transplantation. These post-transplantation complications may be ameliorated once detected at early stages. Therefore, it is essential to monitor post-transplantation conditions in order to alleviate adverse complications.

Alterations in the extracellular matrix contribute to the interstitial remodeling in post-transplantation complications. Matrix metalloproteinases (MMPs) are involved in both the turnover and degradation of extracellular matrix (ECM) proteins. MMPs are a family of proteolytic, zinc-dependent enzymes, with 27 members described to date, displaying multidomain structures and substrate specificities, and functioning in the processing, activation, or deactivation of a variety of soluble factors. Serum MMP levels may indicate the status of post-transplantation conditions. Indeed, circulating MMP-2 is associated with cystatin C, posttransplant duration, and diabetes mellitus in kidney transplant recipients (Chang et al., 2008). Disproportional expression of MMP-9 is linked to the development of bronchiolitis obliterans syndrome after lung transplantation (Hubner et al., 2005).

MMP mRNAs (MMP1, 8, 12, 15, 20, 21, 24, 26 and 27) can be detected in exosomes shed by glioblastoma cells as shown in Example 4 and Table 10. The present exosome method, isolating exosomes from a bodily fluid and analyzing nucleic acids from said exosomes, can be used to monitor transplantation conditions. The exosome isolation procedure is similar to that detailed in Example 2. The present procedures to analyze nucleic acid contained within exosomes are detailed in Example 9. A significant increase in the expression level of MMP-2 after kidney transplantation will indicate the onset and/or deterioration of post-transplantation complications. Similarly, a significantly elevated level of MMP-9 after lung transplantation, suggests the onset and/or deterioration of bronchiolitis obliterans syndrome.

Therefore, the exosome method can be used to monitor post-transplantation conditions by determining the expression levels of MMP proteins associated with post-transplantation complications. It is also expected that the method can be extrapolated to monitor post-transplantation conditions by determining the expression of other marker genes as well as monitor other medical conditions by determining the genetic profile of nucleic acids associated with these medical conditions.

Examples 16-18. Microvesicles can be Therapeutic Agents or Delivery Vehicles of Therapeutic Agents Example 16: Microvesicle Proteins Induce Angiogenesis In Vitro

A study was designed and carried out to demonstrate glioblastoma microvesicles contribute to angiogenesis. HBMVECs (30,000 cells), a brain endothelial cell line, (Cell Systems, Catalogue #ACBRI-376, Kirkland, Wash., USA) were cultured on Matrigel-coated wells in a 24-well plate in basal medium only (EBM) (Lonza Biologics Inc., Portsmouth, N.H., USA), basal medium supplemented with glioblastoma microvesicles (EBM+MV) (7 μg/well), or basal medium supplemented with a cocktail of angiogenic factors (EGM; hydrocortisone, EGF, FGF, VEGF, IGF, ascorbic acid, FBS, and heparin; Singlequots (EBM positive control). Tubule formation was measured after 16 hours and analyzed with the Image J software. HBMVECs cultured in the presence of glioblastoma microvesicles demonstrated a doubling of tubule length within 16 hours. The result was comparable to the result obtained with HBMCECs cultured in the presence of angiogenic factors (FIG. 18a ). These results show that glioblastoma-derived microvesicles play a role in initiating angiogenesis in brain endothelial cells.

Levels of angiogenic proteins in microvesicles were also analyzed and compared with levels in glioblastoma donor cells. Using a human angiogenesis antibody array, we were able to detect 19 proteins involved in angiogenesis. Specifically, total protein from either primary glioblastoma cells or purified microvesicles isolated from said cells were lysed in lysis buffer (Promega, Madison, Wis., USA) and added to the human angiogenesis antibody array (Panomics, Fremont Calif., USA) according to manufacturer's recommendations. The arrays were scanned and analyzed with the Image J software. As shown in FIG. 18b , of the seven of the 19 angiogenic proteins were readily detected in the microvesicles, 6 (angiogenin, IL-6, 1L-8, TIMP-I, VEGF and TIMP-2) were present at higher levels on a total protein basis as compared to the glioblastoma cells (FIG. 18c ). The three angiogenic proteins most enriched in microvesicles compared to tumor cells were angiogenin, IL-6 and 1L-8, all of which have been implicated in glioma angiogenesis with higher levels associated with increased malignancy (25-27).

Microvesicles isolated from primary glioblastoma cells were also found to promote proliferation of a human U87 glioma cell line. In these studies, 100000 U87 cells were seeded in wells of a 24-well plate and allowed to grow for three days (DMEM-5% FBS) or DMEM-5% FBS supplemented with 125 μg microvesicles isolated from primary glioblastoma cells. After three days, untreated U87 cells (FIG. 19a ) were found to be fewer in number as determined using a Burker chamber, than those supplemented with microvesicles (FIG. 19b ). Both non-supplemented and supplemented U87 cells had increased 5- and 8-fold in number over this period, respectively (FIG. 19c ). Thus, glioblastoma microvesicles appear to stimulate proliferation of other glioma cells.

Example 17: Glioblastoma Microvesicles are Taken Up by HBMVECs

To demonstrate that glioblastoma microvesicles are able to be taken up by human brain microvesicular endothelial cells (HBMVECs), purified glioblastoma microvesicles were labeled with PKH67 Green Fluorescent labeling kit (Sigma-Aldrich, St Louis, Mo., USA). The labeled microvesicles were incubated with HBMVEC in culture (5 pg/50,000 cells) for 20 min at 4° C. The cells were washed and incubated at 37° C. for 1 hour. Within 30 min the PKH67-labeled microvesicles were internalized into endosome-like structures within the HBMVECs (FIG. 17a ). These results show that glioblastoma microvesicles can be internalized by brain endothelial cells.

Similar results were obtained when adding the fluorescently labeled microvesicles to primary glioblastoma cells.

Example 18: mRNA Delivered by Glioblastoma Microvesicles can be Translated in Recipient Cells

To determine whether glioblastoma-derived microvesicles mRNA could be delivered to and expressed in recipient cells, primary human glioblastoma cells were infected with a self-inactivating lentivirus vector expressing secreted Gaussia luciferase (Gluc) using a CMV promoter at an infection efficiency of >95%. The cells were stably transduced and generated microvesicles during the subsequent passages (2-10 passages were analyzed). Microvesicles were isolated from the cells and purified as described above. RT-PCR analysis showed that the mRNA for Gluc (555 bp) as well as GAPDH (226 bp) were present in the microvesicles (FIG. 17b ). The level of Gluc mRNA was even higher than that for GAPDH as evaluated with quantitative RT-PCR.

Fifty micrograms of the purified microvesicles were added to 50,000 HBMVE cells and incubated for 24 hrs. The Gluc activity in the supernatant was measured directly after microvesicle addition (0 hrs), and after 15 hrs and 24 hrs. The Gluc activity in the supernatant was normalized to the Gluc protein activity associated with the microvesicles. The results are presented as the mean±SEM (n=4). Specifically, the activity in the recipient HBMVE cells demonstrated a continual translation of the microvesicular Gluc mRNA. Thus, mRNA incorporated into the tumor microvesicles can be delivered into recipient cells and generate a functional protein.

The statistical analyses in all examples were performed using the Student's t-test.

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TABLE 1 RNA in glioblastoma microvesicles can be used as sensitive biomarkers. Time of serum Serum Serum Pa- col- Serum Biopsy exosome exosome tient# lection* volume EGFRvIII EGFRvIII(PP1) EGFRvIII(PP2) 1 0 3 ml Yes Yes — 2 0 2 ml No No — 3 0 2.5 ml No No — 4 0 1 ml Yes No Yes 5 0 1 ml Yes No Yes 6 0 1 ml No No — 7 0 0.6 ml Yes Yes — 8 0 1 ml No No — 9 0 1 ml Yes Yes — 10 0 1 ml No Yes — 11 0 2 ml Yes No Yes 12 0 2 ml Yes Yes — 13 0 2 ml No Yes — 14 0 2 ml Yes Yes — 15 0 2 ml No No — 16 0 2 ml No No — 17 0 1 ml Yes No — 18 0 0.8 ml Yes No — 19 0 1 ml No No — 20 0 1 ml No No — 21 0 1 ml No No — 22 0 1 ml No No — 23 0 1 ml No No — 24 0 1 ml No No — 25 0 1 ml No No — 26 14 0.6 ml Yes No Yes 27 14 1.2 ml No No No 28 14 0.8 ml Yes No Yes 29 14 0.9 ml Yes No No 30 14 0.6 ml Yes No Yes Nested RT-PCR was used to monitor EGFRvIII mRNA in glioma biopsy tissue as well as exosomes purified from a frozen serum sample from the same patient. Samples from 30 patients were analysed in a blinded fashion and PCR reactions were repeated at least three times for each sample. No EGFRvIII mRNA was found in serum microvesicles from 30 normal controls. PP1 refers to primer pair composed of SEQ ID NOs: 13 and 14. PP2 refers to primer pair composed of SEQ ID NOS: 15 and 16. “—” refers to “not available”. *Days post-surgery of tumor removal

TABLE 2 Abbreviations used in Table 3. Abbreviation Term A amplification AEL acute eosinophilic leukemia AL acute leukemia ALCL anaplastic large-cell lymphoma ALL acute lymphocytic leukemia AML acute myelogenous leukemia AML* acute myelogenous leukemia (primarily treatment associated) APL acute promyelocytic leukemia B-ALL B-cell acute lymphocyte leukemia B-CLL B-cell Lymphocytic leukemia B-NHL B-cell Non-Hodgkin Lymphoma CLL chronic lymphatic leukemia CML chronic myeloid leukemia CMML chronic myelomonocytic leukemia CNS central nervous system D large deletion DFSP dermatfibrosarcoma protuberans DLBL diffuse large B-cell lymphoma DLCL diffuse large-cell lymphoma Dom dominant E epithelial F frames GIST gastrointestinal stromal tumour JMML juvenile myelomonocytic leukemia L leukaemia/lymphoma M mesenchymal MALT mucosa-associated lymphoid tissue lymphoma MDS myelodysplastic syndrome Mis Missense MLCLS mediastinal large cell lymphoma with sclerosis MM multiple myeloma MPD Myeloproliferative disorder N nonsense NHL non-Hodgkin lymphoma NK/T natural killer T cell NSCLC non small cell lung cancer O other PMBL primary mediastinal B-cell lymphoma pre-B All pre-B-cell acute lymphablastic leukaemia Rec reccesive S splice site T translocation T-ALL T-cell acute lymphoblastic leukemia T-CLL T-cell chronic lymphocytic leukaemia TGCT testicular germ cell tumour T-PLL T cell prolymphocytic leukaemia

TABLE 3 Genes Commonly Mutated in Cancers Tumour types Tumour types Tissue Cancer Mutation Translocation Symbol Locuslink ID Protein ID* Chromosome band (somatic) (germline) Cancer syndrome type molecular genetics type partner ABL1 25 P00519 9q34.1 CML, ALL — — L Dom T BCR, ETV6 ABL2 27 P42684 1q24-q25 AML — — L Dom T ETV6 AF15Q14 57082 NP_065113 15q14 AML — — L Dom T MLL AF1Q 10962 Q13015 1q21 ALL — — L Dom T MLL AF3p21 51517 Q9NZQ3 3p21 ALL — — L Dom T MLL AF5q31 27125 NP_055238 5q31 ALL — — L Dom T MLL AKT2 208 P31751 19q13.1-q13.2 Ovarian, — — E Dom A pancreatic ALK 238 Q9UM73 2p23 ALCL — — L Dom T NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17 ALO17 57714 XP_290769 17q25.3 ALCL — — L Dom T ALK APC 324 P25054 5q21 Colorectal, Colorectal, Adenomatous E, M, O Rec D^(‡), Mis, N, — pancreatic, pancreatic, polyposis coli; F, S desmoid, desmoid, Turcot hepatoblastoma, hepatoblastoma, syndrome glioma, other glioma, other CNS CNS ARHGEF12 23365 NP_056128 11q23.3 AML — — L Dom T MLL ARHH 399 Q15669 4p13 NHL — — L Dom T BCL6 ARNT 405 P27540 1q21 AML — — L Dom T ETV6 ASPSCR1 79058 NP_076988 17q25 Alveolar soft — — M Dom T TFE3 part sarcoma ATF1 466 P18846 12q13 Malignant — — E, M Dom T EWSR1 melanoma of soft parts, angiomatoid fibrous histiocytoma ATIC 471 P31939 2q35 ALCL — — L Dom T ALK ATM 472 Q13315 11q22.3 T-PLL Leukaemia, Ataxia L, O Rec D, Mis, N, — lymphoma, telangiectasia F, S medulloblastoma, glioma BCL10 8915 O95999 1p22 MALT — — L Dom T IGHα BCL11A 53335 NP_060484 2p13 B-CLL — — L Dom T IGHα BCL11B 64919 NP_612808 14q32.1 T-ALL — — L Dom T TLX3 BCL2 596 P10415 18q21.3 NHL, CLL — — L Dom T IGHα BCL3 602 P20749 19q13 CLL — — L Dom T IGHα BCL5 603 I52586 17q22 CLL — — L Dom T MYC BCL6 604 P41182 3q27 NHL, CLL — — L Dom T, Mis IG loci, ZNFN1A1, LCP1, PIM1, TFRC, MHC2TA, NACA, HSPCB, HSPCA, HIST1H4I, IL21R, POU2AF1, ARHH, EIF4A2 BCL7A 605 NP_066273 12q24.1 B-NHL — — L Dom T MYC BCL9 607 O00512 1q21 B-ALL — — L Dom T IGHα, IGLα BCR 613 P11274 22q11.21 CML, ALL — — L Dom T ABL1, FGFR1 BHD 201163 NP_659434 17p11.2 Renal, Birt-Hogg- E, M Rec? Mis, N, F — fibrofolliculomas, Dube syndrome trichodiscomas BIRC3 330 Q13489 11q22-q23 MALT — — L Dom T MALT1 BLM 641 P54132 15q26.1 — Leukaemia, Bloom L, E Rec Mis, N, F — lymphoma, Syndrome skin squamous cell, other cancers BMPR1A 657 P36894 10q22.3 — Gastrointestinal Juvenile E Rec Mis, N, F — polyps polyposis BRAF 673 P15056 7q34 Melanoma, — — E Dom M — colorectal, papillary thyroid, borderline ovarian, NSCLC, cholangiocarcinoma BRCA1 672 P38398 17q21 Ovarian Breast, ovarian Hereditary E Rec D, Mis, N, — breast/ovarian F, S BRCA2 675 P51587 13q12 Breast, Breast, ovarian, Hereditary L, E Rec D, Mis, N, - F, S ovarian, pancreatic, breast/ ovarian pancreatic leukaemia (FANCB, FANCD1) BRD4 23476 O60885 19p13.1 Lethal midline — — E Dom T NUT carcinoma of young people BTG1 694 P31607 12q22 BCLL — — L Dom T MYC CBFA2T1 862 Q06455 8q22 AML — — L Dom T MLL, RUNX1 CBFA2T3 863 NP_005178 16q24 AML — — L Dom T RUNX1 CBFB 865 Q13951 16q22 AML — — L Dom T MYH11 CBL 867 P22681 11q23.3 AML — — L Dom T MLL CCND1 595 P24385 11q13 CLL, B-ALL, — — L, E Dom T IGHα, FSTL3 breast CDH1 999 P12830 16q22.1 Lobular breast, Gastric Familial E Rec Mis, N, F, S — gastric gastric carcinoma CDK4 1019 P11802 12q14 — Melanoma Familial E Dom Mis — malignant melanoma CDKN2A- 1029 NP_478102 9p21 Melanoma, Melanoma, Familial L, E, M, O Rec D, S — p14^(ARF) multiple pancreatic malignant other melanoma CDKN2A- 1029 P42771 9p21 Melanoma, Melanoma, Familial L, E, M, O Rec D, Mis, N, — p16^(INK4A) multiple pancreatic malignant F, S other melanoma CDX2 1045 Q99626 13q12.3 AML — — L Dom T ETV6 CEBPA 1050 NP_004355 11p15.5 AML, MDS — — L Dom Mis, N, F — CEP1 11064 NP_008949 9q33 MPD/NHL — — L Dom T FGFR1 CHIC2 26511 NP_036242 4q11-q12 AML — — L Dom T ETV6 CHN1 1123 P15882 2q31-q32.1 Extraskeletal — — M Dom T TAF15 myxoid chondrosarcoma CLTC 1213 Q00610 17q11-qter ALCL — — L Dom T ALK COL1A1 1277 P02452 17q21.31-q22 Dermatofibrosarcoma — — M Dom T PDGFB protuberans COPEB 1316 Q99612 10p15 Prostatic, — — E, O Rec Mis, N — glioma COX6C 1345 P09669 8q22-q23 Uterine — — M Dom T HMGA2 leiomyoma CREBBP 1387 Q92793 16p13.3 AL, AML — — L Dom T MLL, MORF, RUNXBP2 CTNNB1 1499 P35222 3p22-p21.3 Colorectal, — — E, M, O Dom H, Mis — ovarian, hepatoblastoma, others CYLD 1540 NP_056062 16q12-q13 Cylindroma Cylindroma Familial E Rec Mis, N, F, — cylindromatosis S D10S170 8030 NP_005427 10q21 Papillary — — E Dom T RET, PDGFRB thyroid, CML DDB2 1643 Q92466 11p12 — Skin basal cell, Xeroderma E Rec M, N — skin pigmentosum E squamous cell, melanoma DDIT3 1649 P35638 12q13.1-q13.2 Liposarcoma — — M Dom T FUS DDX10 1662 Q13206 11q22-q23 AML^(§) — — L Dom T NUP98 DEK 7913 P35659 6p23 AML — — L Dom T NUP214 EGFR 1956 P00533 7p12.3-p12.1 Glioma — — O Dom A, O^(∥) — EIF4A2 1974 Q14240 3q27.3 NHL — — L Dom T BCL6 ELKS 23085 NP_055879 12p13.3 Papillary — — E Dom T RET thyroid ELL 8178 P55199 19p13.1 AL — — L Dom T MLL EP300 2033 Q09472 22q13 Colorectal — — L, E Rec T MLL, RUNXBP2 breast, pancreatic, AML EPS15 2060 P42566 1p32 ALL — — L Dom T MLL ERBB2 2064 P04626 17q21.1 Breast, — — E Dom A — ovarian, other tumour types ERCC2 2068 P18074 19q13.2-q13.3 — Skin basal cell, Xeroderma E Rec M, N, F, S — skin pigmentosum D squamous cell, melanoma ERCC3 2071 P19447 2q21 — Skin basal cell, Xeroderma E Rec M, S — skin pigmentosum B squamous cell, melanoma ERCC4 2072 Q92889 16p13.3- — Skin basal cell, Xeroderma E Rec M, N, F — skin pigmentosum F squamous cell, melanoma ERCC5 2073 P28715 13q33 — Skin basal cell, Xeroderma E Rec M, N, F — skin pigmentosum G squamous cell, melanoma ERG 2078 P11308 21q22.3 Ewing's sarcoma — — M Dom T EWSR1 ETV1 2115 P50549 7p22 Ewing's sarcoma — — M Dom T EWSR1 ETV4 2118 P43268 17q21 Ewing's sarcoma — — M Dom T EWSR1 ETV6 2120 P41212 12p13 Congenital — — L, E, M Dom T NTRK3, RUNX1, fibrosarcoma, PDGFRB, multiple ABL1, MN1, leukaemia ABL2, FACL6, and lymphoma, CHIC2, ARNT, secretory JAK2, EVI1, breast CDX2, STL EVI1 2122 Q03112 3q26 AML, CML — — L Dom T RUNX1, ETV6 EWSR1 2130 NP_005234 22q12 Ewing's — — L, M Dom T FLI1, ERG, sarcoma, ZNF278, desmoplastic NR4A3, TEC, small FEV, ATF1, round cell, ETV1, ETV4, ALL WT1, ZNF384 EXT1 2131 NP_000118 8q24.11-q24.13 — Exostoses, Multiple M Rec Mis, N, F, — osteosarcoma exostoses S type 1 EXT2 2132 Q93063 11p12-p11 — Exostoses, Multiple M Rec Mis, N, F, — osteosarcoma exostoses S type 2 FACL6 23305 NP_056071 5q31 AML, AEL — — L Dom T ETV6 FANCA 2175 NP_000126 16q24.3 — AML, leukaemia Fanconi L Rec D, Mis, N, — anaemia A F, S FANCC 2176 Q00597 9q22.3 — AML, leukaemia Fanconi L Rec D, Mis, N, — anaemia C F, S FANCD2 2177 NP_149075 3p26 — AML, leukaemia Fanconi L Rec D, Mis, N, — anaemia D2 F FANCE 2178 NP_068741 6p21-p22 — AML, leukaemia Fanconi L Rec N, F, S — anaemia E FANCF 2188 Q9NPI8 11p15 — AML, leukaemia Fanconi L Rec N, F — anaemia F FANCG 2189 O15287 9p13 — AML, leukaemia Fanconi L Rec Mis, N, F, — anaemia G S FEV 54738 NP_059991 2q36 Ewing's sarcoma — — M Dom T EWSR1 FGFR1 2260 P11362 8p11.2-p11.1 MPD/NHL — — L Dom T BCR, FOP, ZNF198, CEP1 FGFR1OP 11116 NP_008976 6q27 MPD/NHL — — L Dom T FGFR1 FGFR2 2263 P21802 10q26 Gastric — — E Dom Mis — FGFR3 2261 P22607 4p16.3 Bladder, MM — — L, E Dom Mis, T IGHα FH 2271 P07954 1q42.1 — Leiomyomatosis, Hereditary E, M Rec Mis, N, F — renal leiomyomatosis and renal-cell cancer FIP1L1 81608 NP_112179 4q12 Idiopathic — — L Dom T PDGFRA hypereosinophilic syndrome FLI1 2313 Q01543 11q24 Ewing's sarcoma — — M Dom T EWSR1 FLT3 2322 P36888 13q12 AML, ALL — — L Dom Mis, O — FLT4 2324 P35916 5q35.3 Angiosarcoma — — M Dom Mis — FNBP1 23048 XP_052666 9q23 AML — — L Dom T MLL FOXO1A 2308 Q12778 13q14.1 Alveolar — — M Dom T PAX3 rhabdomyosarcomas — — FOXO3A 2309 O43524 6q21 AL — — L Dom T MLL FSTL3 10272 O95633 19p13 B-CLL — — L Dom T CCND1 FUS 2521 P35637 16p11.2 Liposarcoma — — M Dom T DDIT3 GAS7 8522 O60861 17p AML^(§) — — L Dom T MLL GATA1 2623 P15976 Xp11.23 Megakaryoblastic — — L Dom Mis, F — leukaemia of Down syndrome GMPS 8833 P49915 3q24 AML — — L Dom T MLL GNAS 2778 P04895 20q13.2 Pituitary — — E Dom Mis — adenoma GOLGA5 9950 NP_005104 14q Papillary — — E Dom T RET thyroid GPC3 2719 P51654 Xq26.1 — Wilms' tumour Simpson- O Rec T, D, Mis, — Golabi-Behmel N, F, S O syndrome GPHN 10243 Q9NQX3 14q24 AL — — L Dom T MLL GRAF 23092 NP_055886 5q31 AML, MDS — — L Dom T, F, S MLL HEI10 57820 NP_067001 14q11.1 Uterine — — M Dom T HMGA2 leiomyoma HIP1 3092 O00291 7q11.23 CMML — — L Dom T PDGFRB HIST1H4I 8294 NP_003486 6p21.3 NHL — — L Dom T BCL6 HLF 3131 Q16534 17q22 ALL — — L Dom T TCF3 HMGA2 8091 P52926 12q15 Lipoma — — M Dom T LHFP, RAD51L1, LPP, HEI10, COX6C HOXA11 3207 P31270 7p15-p14.2 CML — — L Dom T NUP98 HOXA13 3209 P31271 7p15-p14.2 AML — — L Dom T NUP98 HOXA9 3205 P31269 7p15-p14.2 AML^(§) — — L Dom T NUP98 HOXC13 3229 P31276 12q13.3 AML — — L Dom T NUP98 HOXD11 3237 P31277 2q31-q32 AML — — L Dom T NUP98 HOXD13 3239 P35453 2q31-q32 AML^(§) — — L Dom T NUP98 HRAS 3265 P01112 11p15.5 Infrequent — — L, M Dom Mis — sarcomas, rare other types HRPT2 3279 NP_013522 1q21-q31 Parathyroid Parathyroid Hyperpara- E, M Rec Mis, N, F — adenoma adenoma, thyroidism jaw multiple tumour ossifying syndrome jaw fibroma HSPCA 3320 P07900 1q21.2-q22 NHL — — L Dom T BCL6 HSPCB 3326 P08238 6p12 NHL — — L Dom T BCL6 IGHα 3492 — 14q32.33 MM, Burkitt's — — L Dom T MYC, FGFR3, lymphoma, NHL, PAX5, IRTA1, CLL, B-ALL, IRF4, CCND1, MALT BCL9, BCL6, BCL8, BCL2, BCL3, BCL10, BCL11A. LHX4 IGKα 50802 — 2p12 Burkitt's — — L Dom T MYC lymphoma IGLα 3535 — 22q11.1-q11.2 Burkitt's — — L Dom T BCL9, MYC lymphoma IL21R 50615 Q9HBE5 16p11 NHL — — L Dom T BCL6 IRF4 3662 Q15306 6p25-p23 MM — — L Dom T IGHα IRTA1 83417 NP_112572 1q21 B-NHL — — L Dom T IGHα JAK2 3717 O60674 9p24 ALL, AML — — L Dom T ETV6 KIT 3815 P10721 4q12 GIST, AML, GIST, Familial L, M, O Dom Mis, O — TGCT epithelioma gastrointestinal stromal KRAS2 3845 NP_004976 12p12.1 Pancreatic, — — L, E, Dom Mis — colorectal, M, O lung, thyroid, AML, others LAF4 3899 P51826 2q11.2-q12 ALL — — L Dom T MLL LASP1 3927 Q14847 17q11-q21.3 AML — — L Dom T MLL LCK 3932 NP_005347 1p35-p34.3 T-ALL — — L Dom T TRBα LCP1 3936 P13796 13q14.1-q14.3 NHL — — L Dom T BCL6 LCX 80312 XP_167612 10q21 AML — — L Dom T MLL LHFP 10186 NP_005771 13q12 Lipoma — — M Dom T HMGA2 LMO1 4004 P25800 11p15 T-ALL — — L Dom T TRDα LMO2 4005 P25791 11p13 T-ALL — — L Dom T TRDα LPP 4026 NP_005569 3q28 Lipoma, — — L, M Dom T HMGA2, MLL leukaemia LYL1 4066 P12980 19p13.2-p13.1 T-ALL — — L Dom T TRBα MADH4 4089 Q13485 18q21.1 Colorectal, Gastrointestinal Juvenile E Rec D, Mis, N, — pancreatic, polyps polyposis F small intestine MALT1 10892 Q9UDY8 18q21 MALT — — L Dom T BIRC3 MAML2 84441 XP_045716 11q22-q23 Salivary-gland — — E Dom T MECT1 mucoepidermoid MAP2K4 6416 P45985 17p11.2 Pancreatic, — — E Rec D, Mis, N — breast, colorectal MDS1 4197 Q13465 3q26 MDS, AML — — L Dom T RUNX1 MECT1 94159 AAK93832.1 19p13 Salivary-gland — — E Dom T MAML2 mucoepidermoid MEN1 4221 O00255 11q13 Parathyroid Parathyroid Multiple E Rec D, Mis, N, — adenoma, endocrine F, S pituitary neoplasia adenoma, type 1 pancreatic islet cell, carcinoid MET 4233 P08581 7q31 Papillary Papillary Familial E Dom Mis — renal, renal papillary renal head-neck squamous cell MHC2TA 4261 P33076 16p13 NHL — — L Dom T BCL6 MLF1 4291 P58340 3q25.1 AML — — L Dom T NPM1 MLH1 4292 P40692 3p21.3 Colorectal, Colorectal, endometrial, Hereditary non- E, O Rec D, Mis, N, — endometrial, ovarian, CNS polyposis F, S ovarian, CNS colorectal, Turcot syndrome MLL 4297 Q03164 11q23 AML, ALL — — L Dom T, O MLL, MLLT1, MLLT2, MLLT3, MLLT4, MLLT7, MLLT10, MLLT6, ELL, EPS15, AF1Q, CREBBP, SH3GL1, FNBP1, PNUTL1, MSF, GPHN, GMPS, SSH3BP1, ARHGEF12, GAS7, FOXO3A, LAF4, LCX, SEPT6, LPP, CBFA2T1, GRAF, EP300, PICALM MLLT1 4298 Q03111 19p13.3 AL — — L Dom T MLL MLLT10 8028 P55197 10p12 AL — — L Dom T MLL, PICALM MLLT2 4299 P51825 4q21 AL — — L Dom T MLL MLLT3 4300 P42568 9p22 ALL — — L Dom T MLL MLLT4 4301 P55196 6q27 AL — — L Dom T MLL MLLT6 4302 P55198 17q21 AL — — L Dom T MLL MLLT7 4303 NP_005929 Xq13.1 AL — — L Dom T MLL MN1 4330 Q10571 22q13 AML, meningioma — — L, O Dom T ETV6 MSF 10801 NP_006631 17q25 AML^(§) — — L Dom T MLL MSH2 4436 P43246 2p22-p21 Colorectal, Colorectal, Hereditary non- E Rec D, Mis, N — endometrial, endometrial, polyposis F, S ovarian ovarian colorectal MSH6 2956 P52701 2p16 Colorectal Colorectal, Hereditary non- E Rec Mis, N, F, — endometrial, polyposis S ovarian colorectal MSN 4478 P26038 Xq11.2-q12 ALCL — — L Dom T ALK MUTYH 4595 NP_036354 1p343-1p32.1 Colorectal Adenomatous E Rec Mis, N, F, — polyposis coli S MYC 4609 P01106 8q24.12-q24.13 Burkitt's — — L, E Dom A, T IGKα, BCL5, lymphoma, BCL7A, BTG1, amplified in TRAα, IGHα other cancers, B-CLL MYCL1 4610 P12524 1p34.3 Small cell lung — — E Dom A — MYCN 4613 P04198 2p24.1 Neuroblastoma — — O Dom A — MYH11 4629 P35749 16p13.13-p13.12 AML — — L Dom T CBFB MYH9 4627 P35579 22q13.1 ALCL — — L Dom T ALK MYST4 23522 NP_036462 10q22 AML — — L Dom T CREBBP NACA 4666 NP_005585 12q23-q24.1 NHL — — L Dom T BCL6 NBS1 4683 NP_002476 8q21 — NHL, glioma, Nijmegen L, E, M, O Rec Mis, N, F — medulloblastoma, breakage rhabdomyosarcoma syndrome NCOA2 10499 Q15596 8q13.1 AML — — L Dom T RUNXBP2 NCOA4 8031 Q13772 10q11.2 Papillary — — E Dom T RET thyroid NF1 4763 P21359 17q12 Neurofibroma, Neurofibroma, Neurofibromatosis O Rec D, Mis, N, — glioma glioma type 1 F, S, O NF2 4771 P35240 22q12.2 Meningioma, Meningioma, Neurofibromatosis O Rec D, Mis, N, — acoustic acoustic type 2 F, S, O neuroma neuroma NOTCH1 4851 P46531 9q34.3 T-ALL — — L Dom T TRBα NPM1 4869 P06748 5q35 NHL, APL, AML — — L Dom T ALK, RARA, MLF1 NR4A3 8013 Q92570 9q22 Extraskeletal — — M Dom T EWSR1 myxoid chondrosarcoma NRAS 4893 P01111 1p13.2 Melanoma, MM, — — L, E Dom Mis — AML, thyroid NSD1 64324 NP_071900 5q35 AML — — L Dom T NUP98 NTRK1 4914 P04629 1q21-q22 Papillary — — E Dom T TPM3, TPR, thyroid TFG NTRK3 4916 Q16288 15q25 Congenital — — E, M Dom T ETV6 fibrosarcoma, secretory breast NUMA1 4926 NP_006176 11q13 APL — — L Dom T RARA NUP214 8021 P35658 9q34.1 AML — — L Dom T DEK, SET NUP98 4928 P52948 11p15 AML — — L Dom T HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1 NUT 256646 XP_171724 15q13 Lethal midline — — E Dom T BRD4 carcinoma of young people OLIG2 10215 Q13516 21q22.11 T-ALL — — L Dom T TRAα PAX3 5077 P23760 2q35 Alveolar — — M Dom T FOXO1A rhabdomyosarcoma PAX5 5079 Q02548 9p13 NHL — — L Dom T IGHα PAX7 5081 P23759 1p36.2-p36.12 Alveolar — — M Dom T FOXO1A rhabdomyosarcoma PAX8 7849 Q06710 2q12-q14 Follicular thyroid — — E Dom T PPARG PBX1 5087 NP_002576 1q23 Pre-B-ALL — — L Dom T TCF3 PCM1 5108 NP_006188 8p22-p21.3 Papillary thyroid — — E Dom T RET PDGFB 5155 P01127 22q12.3-q13.1 DFSP — — M Dom T COL1A1 PDGFRA 5156 P16234 4q11-q13 GIST — — M, O Dom Mis, O — PDGFRB 5159 NP_002600 5q31-q32 MPD, AML, — — L Dom T ETV6, TRIP11, CMML, CML HIP1, RAB5EP, H4 PICALM 8301 Q13492 11q14 T-ALL, AML — — L Dom T MLLT10, MLL PIM1 5292 P11309 6p21.2 NHL — — L Dom T BCL6 PML 5371 P29590 15q22 APL — — L Dom T RARA PMS1 5378 P54277 2q31-q33 — Colorectal, Hereditary non- E Rec Mis, N — endometrial, polyposis ovarian colorectal cancer PMS2 5395 P54278 7p22 — Colorectal, Hereditary non- E Rec Mis, N, F — endometrial, polyposis ovarian, colorectal medulloblastoma, cancer, Turcot glioma syndrome PMX1 5396 P54821 1q24 AML — — L Dom T NUP98 PNUTL1 5413 NP_002679 22q11.2 AML — — L Dom T MLL POU2AF1 5450 Q16633 11q23.1 NHL — — L Dom T BCL6 PPARG 5468 P37231 3p25 Follicular — — E Dom T PAX8 thyroid PRCC 5546 Q92733 1q21.1 Papillary renal — — E Dom T TFE3 PRKAR1A 5573 P10644 17q23-q24 Papillary Myxoma, Carney complex E, M Dom, Rec T, Mis, N, RET thyroid endocrine, F, S papillary thyroid PRO1073 29005 Q9UHZ2 11q31.1 Renal-cell — — E Dom T TFEB carcinoma (childhood epithelioid) PSIP2 11168 NP_150091 9p22.2 AML — — L Dom T NUP98 PTCH 5727 Q13635 9q22.3 Skin basal cell, Skin basal cell, Nevoid basal- E, M Rec Mis, N, F, — medulloblastoma medulloblastoma cell carcinoma S syndrome PTEN 5728 O00633 10q23.3 Glioma, Harmartoma, Cowden L, E, M, O Rec D, Mis, N, — prostatic, glioma, syndrome, F, S endometrial prostatic, Bannayan- endometrial Riley- Ruvalcaba syndrome PTPN11 5781 Q06124 12q24.1 JMML, AML, — — L Dom T Mis — MDS RAB5EP 9135 NP_004694 17p13 CMML — — L Dom T PDGFRB RAD51L1 5890 NP_002868 14q23-q24.2 Lipoma, uterine — — M Dom T HMGA2 leiomyoma RAP1GDS1 5910 P52306 4q21-q25 T-ALL — — L Dom T NUP98 RARA 5914 P10276 17q12 APL — — L Dom T PML, ZNF145, TIF1, NUMA1, NPM1 RB1 5925 P06400 13q14 Retinoblastoma, Retinoblastoma, Familial L, E, M, O Rec D, Mis, N, — sarcoma, breast, sarcoma, breast, retinoblastoma F, S small-cell lung small-cell lung RECQL4 9401 O94761 8q24.3 — Osteosarcoma, Rothmund- M Rec N, F, S — skin basal Thompson and squamous cell syndrome REL 5966 Q04864 2p13-p12 Hodgkin — — L Dom A — Lymphoma RET 5979 P07949 10q11.2 Medullary Medullary Multiple E, O Dom T, Mis, N, H4, PRKAR1A, thyroid, thyroid, endocrine F NCOA4, PCM1, papillary papillary 2A/2B GOLGA5,TRIM33 thyroid, thyroid, pheochromocytoma pheochromo- cytomaneoplasia RPL22 6146 P35268 3q26 AML, CML — — L Dom T RUNX1 RUNX1 861 Q01196 21q22.3 AML, pre-B-ALL — — L Dom T RPL22, MDS1 EVI1, CBFA2T3, CBFA2T1, ETV6 RUNXBP2 799 NP_006757 8p11 AML — — L Dom T CREBBP, NCOA2, EP300 SBDS 51119 Q9Y3A5 7q11 — AML, MDS Schwachman- L Rec Gene — Diamond conversion syndrome SDHB 6390 P21912 1p36.1-p35 — Paraganglioma, Familial O Rec Mis, N, F — pheochromocytoma paraganglioma SDHC 6391 O75609 1q21 — Paraganglioma, Familial O Rec Mis, N, F — pheochromocytoma paraganglioma SDHD 6392 O14521 11q23 — Paraganglioma, Familial O Rec Mis, N, F, — pheochromocytoma paraganglioma S SEPT6 23157 NP_055944 Xq24 AML — — L Dom T MLL SET 6418 Q01105 9q34 AML — — L Dom T NUP214 SFPQ 6421 P23246 1p34.3 Papillary renal — — E Dom T TFE3 cell SH3GL1 6455 Q99961 19p13.3 AL — — L Dom T MLL SMARCB1 6598 Q12824 22q11 Malignant Malignant Rhabdoid M Rec D, N, F, — rhabdoid rhabdoid predisposition S syndrome SMO 6608 Q99835 7q31-q32 Skin basal cell — — E Dom Mis — SS18 6760 Q15532 18q11.2 Synovial sarcoma — — M Dom T SSX1, SSX2 SS18L1 26039 O75177 20q13.3 Synovial sarcoma — — M Dom T SSX1 SSH3BP1 10006 NP_005461 10p11.2 AML — — L Dom T MLL SSX1 6756 Q16384 Xp11.23-p11.22 Synovial sarcoma — — M Dom T SS18 SSX2 6757 Q16385 Xp11.23-p11.22 Synovial sarcoma — — M Dom T SS18 SSX4 6759 O60224 Xp11.23 Synovial sarcoma — — M Dom T SS18 STK11 6794 Q15831 19p13.3 NSCLC Jejunal Peutz-Jeghers E, M, O Rec D, Mis, N, — harmartoma, syndrome ovarian, testicular, pancreatic STL 7955 NOPROTEIN 6q23 B-ALL — — L Dom T ETV6 SUFU 51684 NP_057253 10q24.32 Medulloblastoma Medulloblastoma Medulloblastoma O Rec D, F, S — predisposition TAF15 8148 Q92804 17q11.1-q11.2 Extraskeletal — — L, M Dom T TEC, CHN1, myxoid ZNF384 chondrosarcomas, ALL TAL1 6886 P17542 1p32 Lymphoblastic — — L Dom T TRDα leukaemia/biphasic TAL2 6887 Q16559 9q31 T-ALL — — L Dom T TRBα TCF1 6927 P20823 12q24.2 Hepatic adenoma, Hepatic adenoma, Familial hepatic E Rec Mis, F — hepatocellular hepatocellular adenoma carcinoma carcinoma TCF12 6938 Q99081 15q21 Extraskeletal — — M Dom T TEC myxoid chondrosarcoma TCF3 6929 P15923 19p13.3 pre-B-ALL — — L Dom T PBX1, HLF, TFPT TCL1A 8115 NP_068801 14q32.1 T-CLL — — L Dom T TRAα TEC 7006 P42680 4p12 Extraskeletal — — M Dom T EWSR1, TAF15, myxoid TCF12 chondrosarcoma TFE3 7030 P19532 Xp11.22 Papillary renal, — — E Dom T SFPQ, alveolar soft part ASPSCR1, sarcoma PRCC TFEB 7942 P19484 6p21 Renal (childhood — — E, M Dom T ALPHA epithelioid) TFG 10342 NP_006061 3q11-q12 Papillary thyroid, — — E, L Dom T NTRK1, ALK ALCL TFPT 29844 NP_037474 19q13 Pre-B-ALL — — L Dom T TCF3 TFRC 7037 P02786 3q29 NHL — — L Dom T BCL6 TIF1 8805 O15164 7q32-q34 APL — — L Dom T RARA TLX1 3195 P31314 10q24 T-ALL — — L Dom T TRBα, TRDα TLX3 30012 O43711 5q35.1 T-ALL — — L Dom T BCL11B TNFRSF6 355 P25445 10q24.1 TGCT, nasal NK/T — — L, E, O Rec Mis — lymphoma, skin squamous-cell carcinoma (burn- scar related) TOP1 7150 P11387 20q12-q13.1 AML^(§) — — L Dom T NUP98 TP53 7157 P04637 17p13 Breast, colorectal, Breast, sarcoma, Li-Fraumeni L, E, M, O Rec Mis, N, F — lung, sarcoma, adrenocortical syndrome adrenocortical, carcinoma, glioma, multiple glioma, multiple other types other types TPM3 7170 P06753 1q22-q23 Papillary thyroid, — — E, L Dom T NTRK1, ALK ALCL TPM4 7171 P07226 19p13.1 ALCL — — L Dom T ALK TPR 7175 P12270 1q25 Papillary thyroid — — E Dom T NTRK1 TRAα 6955 — 14q11.2 T-ALL — — L Dom T ATL, OLIG2, MYC, TCL1A TRBα 6957 — 7q35 T-ALL — — L Dom T HOX11, LCK, NOTCH1, TAL2, LYL1 TRDα 6964 — 14q11 T-cell leukaemia — — L Dom T TAL1, HOX11, TLX1, LMO1, LMO2 TRIM33 51592 Q9UPN9 1p13 Papillary thyroid — — E Dom T RET TRIP11 9321 NP_004230 14q31-q32 AML — — L Dom T PDGFRB TSC1 7248 Q92574 9q34 — Hamartoma, renal Tuberous E, O Rec D, Mis, N, — cell sclerosis 1 F, S TSC2 7249 P49815 16p13.3 — Hamartoma, renal Tuberous E, O Rec D, Mis, N, — cell sclerosis 2 F, S TSHR 7253 P16473 14q31 Toxic thyroid Thyroid adenoma — E Dom Mis — adenoma VHL 7428 P40337 3p25 Renal, Renal, von Hippel- E, M, O Rec D, Mis, N, — hemangioma, hemangioma, Lindau F, S pheochromocytoma pheochromocytoma syndrome WAS 7454 P42768 Xp11.23-p11.22 — Lymphoma Wiskott-Aldrich L Rec Mis, N, F, — syndrome S WHSC1L1 54904 NP_060248 8p12 AML — — L Dom T NUP98 WRN 7486 Q14191 8p12-p11.2 — Osteosarcoma, Werner L, E, M, Rec Mis, N, F, — meningioma, syndrome O S others WT1 7490 NP_000369 11p13 Wilms', Wilms' Denys-Drash O Rec D, Mis, N, EWSR1 desmoplastic small syndrome, F, S round cell Frasier syndrome, Familial Wilms' tumour XPA 7507 P23025 9q22.3 — Skin basal cell, Xeroderma E Rec Mis, N, F, — skin pigmentosum A S squamous cell, melanoma XPC 7508 Q01831 3p25 — Skin basal cell, Xeroderma E Rec Mis, N, F, — skin pigmentosum C S squamous cell, melanoma ZNF145 7704 Q05516 11q23.1 APL — — L Dom T RARA ZNF198 7750 Q9UBW7 13q11-q12 MPD/NHL — — L Dom T FGFR1 ZNF278 23598 NP_055138 22q12-q14 Ewing's sarcoma — — M Dom T EWSR1 ZNF384 171017 NP_597733 12p13 ALL — — L Dom T EWSR1, TAF15 ZNFN1A1 10320 NP_006051 7p12 ALL, DLBCL — — L Dom T BCL6 *From Swiss-Prot/Refseq. ^(‡)D (large deletion) covers the abnormalities that result in allele loss/loss of heterozygosity at many recessive cancer genes. ^(§)Refers to cases of acute myeloid leukaemia that are associated with treatment. ^(∥)O (other) in the ‘mutation type’ column refers primarily to small in-frame deletions/insertions as found in KIT/PDGFRA, and larger duplications/insertions as found in FLT3 and EGFR. Note that where an inversion/large deletion has been shown to result in a fusions protein, these have been listed under translocations. The Wellcome Trust Sanger Institute web version of the cancer-gene set can be found at http://www.sanger.ac.uk/genetics/CPG/Census/. A, amplification; AEL, acute eosinophilic leukaemia; AL, acute leukaemia; ALCL, anaplastic large-cell lymphoma; ALL, acute lymphocytic leukaemia; AML, acute myelogenous leukaemia; APL, acute promyelocytic leukaemia; B-ALL, B-cell acute lymphocytic leukaemia; B-CLL, B-cell lymphocytic leukaemia; B-NHL, B-cell non-Hodgkin's lymphoma; CLL, chronic lymphatic leukaemia; CML, chronic myeloid leukaemia; CMML, chronic myelomonocytic leukaemia; CNS, central nervous system; D, large deletion; DFSP, dermatofibrosarcoma protuberans; DLBCL, diffuse large B-cell lymphoma; Dom, dominant; E, epithelial; F, frameshift; GIST, gastrointestinal stromal tumour; JMML, juvenile myelomonocytic leukaemia; L, leukaemia/lymphoma; M, mesenchymal; MALT, mucosa-associated lymphoid tissue; MDS, myelodysplastic syndrome; MM, multiple myeloma; Mis, missense; N, nonsense; NHL, non-Hodgkin's lymphoma; NK/T, natural killer T cell; NSCLC, non-small-cell lung cancer; O, other; pre-B-ALL, pre-B-cell acute lymphoblastic leukaemia; Rec, recessive; S, splice site; T, translocation; T-ALL, T-cell acute lymphoblastic leukaemia; T-CLL, T-cell chronic lymphocytic leukaemia; TGCT, testicular germ-cell tumour; T-PLL, T-cell prolymphocytic leukaemia.

TABLE 4 Commonly Upregulated Genes in Cancers Gene Gene UnlGene symbol p # Down # UniGene symbol p # Down # Hs. 15943O FNDC3B 1 00 Hs. 239388 PAQR8 1 Hs. 518201 DTX3L 0 Hs. 592827 RBAK 1 Hs. 530899 LOC162073 0 Hs. 525157 TNFSF13B 1 Hs. 15159 CKLF 1 1 Hs. 126774 DTL 3 0 Hs. 474150 BID 6 03 Hs. 385913 ANP32E 3 1 Hs. 7753 CALU 5 02 Hs. 532968 DKFP762E1312 3 1 Hs. 418795 GLT2SDI 0 0 Hs. 372429 PDIA6 3 1 Hs 435556 BFAR 2 0 Hs. 233952 PSMA7 3 1 Hs. 459362 PACI 2 1 Hs. 533770 SLC38A1 3 1 Hs. 521800 Cborf76 0 Hs. 489284 ARPC18 8 01 Hs. 209561 KIAA1715 0 Hs. 497788 EPRS 8 01 Hs. 585011 C1orf96 1 Hs. 79110 NCL 8 01 Hs. .403933 FBX032 1 Hs. 251531 PSMA4 8 01 Hs. 368853 AYTL2 5 11 Hs. 429180 Elf2S2 8 11 Hs. 511093 NUSAP1 1 0 Hs. 46S885 ILF3 8 11 Hs. 370895 RPN2 4 00 Hs. 169840 TTK 8 11 Hs. 180062 PSMBB 7 02 Hs. 489365 APIST 5 1 Hs. 444600 BOLAZ 0 0 Hs. 256639 PPIH 5 1 Hs. 44589O CHIH4 3 0 Hs. 14559 CEP55 0 1 Hs. 534392 KDELR3 3 0 Hs. 308613 MTERFD1 0 1 Hs. 632191 XTP3TPA 3 0 Hs. 21331 ZWlLCH 0 1 Hs. 387567 ACLV 9 13 Hs. 524S99 NAPIL! 7 10 Hs. 533282 NONO 8 02 Hs. 78171 PGK1 7 20 Hs. 83753 SNRPB 8 02 Hs. 512380 PLEKHB2 2 1 Hs. 471441 PSMBZ 8 12 Hs. 352018 TAP1 9 11 Hs. 482497 TNPOI 8 12 Hs. 194698 CCNB2 4 1 Hs. 370937 TAPBP 5 00 Hs. 153357 PLOD3 4 1 Hs .126941 FAM49B 2 0 Hs. 471200 NRP2 4 2 Hs. 408629 KDELCI 2 0 Hs. 250822 AURKA 6 1 Hs. 49?384 IPO9 2 1 Hs. 75528 GNl2 6 1 Hs. 8752 TMEM4 2 1 Hs. 1197 HSPEI 6 1 Hs. 195642 C17orf27 0 Hs. 202672 DNMTI 8 10 Hs. 358997 TTL 0 Hs. 433670 FTL 8 10 Hs. l600 CCT5 0 03 Hs. 519972 HLA-F 8 10 Hs. 269408 E2F3 7 01 HS. 520210 KDELR2 8 10 Hs. 234027 ZBTB12 7 11 Hs. 40515.1 CARD-4 1 1 Hs. 520205 EIF2AK1 4 0 Hs. 477700 DBRI 1 1 Hs. 89545 PSMB4 4 0 Hs. I4468 FLJ11286 1 1 Hs. 449415 EIF2C2 4 1 Hs. 516077 FLJ14668 1 1 Hs. 409065 FEN1 4 1 HS. 494337 GOLPH2 1 1 Hs. 313 SPP1 4 2 Hs.. 371036 NOX4 1 1 Hs. .525135 FARP1 4 2 Hs. .438683 SLAMF8 1 1 Hs. 524390 K-ALPHA-1 1 0 Hs. 520714 SNXIO 1 1 Hs. .432360 SCNM1 1 0 Hs. 159428 BAX 3 1 Hs. 172028 ADAM10 9 02 Hs. .311609 DDX39 3 1 Hs. 381189 CBX3 9 02 Hs. 463035 FKBP10 3 1 Hs. 522257 HNRPK 9 02 Hs. 438695 FKBP11 3 1 Hs. 470943 STATI 9 02 Hs. 515255 LSM4 3 1 Hs. 118638 NME1 9 12 Hs. 55285 MORC2 3 1 Hs. 519452 NPM1 9 12 Hs. 43666 PTP4A3 3 1 Hs. 506748 HDGF 6 00 Hs. 369440 SFXN1 3 1 Hs. 386283 ADAM12 6 20 Hs. 517155 TMEPAI 3 1 Hs. 474740 APOL2 0 Hs. 631580 UBA2 3 1 Hs. 552608 C1orf58 0 Hs. 46346S UTP16 3 1 Hs. 470654 CDCA7 0 Hs. 492974 WISP1 3 1 Hs. 179′B8 FMNL3 0 Hs. 113876 WHSC1 3 1 Hs. 143618 GEMIN6 0 Hs. 494614 BAT2D1 5 2 Hs. 6459 GPRI72A 0 Hs. 166463 HNRPU 9 20 Hs. 133294 IQGAP3 0 No number of studies (types of cancer) which have available expression data on a test gene. Up # or down # number of cancer types whose expression of the tested gene is up or down -regulated. All these genes are significantly consistently up-regulated (P < 10) in a large majority of cancer types. doi: 10.137/journal pone. 0001149.001

TABLE 5 Commonly Downregulated Genes in Cancers Gene Gene UnlGene symbol p # Down # UniGene symbol p # Down # Hs. 401835 TCEA12 0 8 Hs. 306083 LOC91689 5 Hs. 58351 ABCA8 3 10 Hs. 160953 PS3AIP1 5 Hs. 525205 NDRG2 2 9 Hs. 2112252 SLC24A3 5 Hs. 524085 USP2 2 9 Hs. 163079 TUBAL3 5 Hs. 172755 BRP44L 1 8 Hs. 389171 PINK1 3 8 Hs. 22242 ECHDC3 1 8 Hs. 470887 GULP1 3 8 Hs. 196952 HLF 9 13 Hs. 490981 MSRA 3 8 Hs. 496587 CHRDL1 2 8 Hs. 476092 CLEC3B 8 11 Hs. 476319 ECHDC2 2 8 Hs. 386502 FMO4 8 11 Hs. 409352 FLJ20701 2 8 Hs. 137367 ANK2 8 11 Hs. 103253 PLIN 2 8 Hs. 212088 EPHX2 8 11 Hs. 293970 ALDH6A1 8 12 Hs. 157818 KCNAB1 8 11 Hs. 390729 ERBB4 7 11 Hs. 163924 NR3C2 8 11 Hs. 553502 RORA 7 11 Hs. 269128 PPP2R1B 8 11 Hs. 388918 RECK 4 9 Hs. 40582 CDC148 5 9 Hs. 216226 SYNGR1 4 9 Hs. 438867 FL20489 0 6 Hs. 506357 fam107a 4 9 Hs. 224008 FEZ1 7 10 Hs. 476454 ABHD6 1 7 Hs. 443789 C6orf60 2 7 Hs. 519694 Csorf4 1 7 Hs. 475319 LRRFIP2 2 7 Hs. 528385 DHR54 1 7 Hs. 514713 MPPE1 2 7 Hs. 477288 TRPM3 7 Hs. 183153 ARL4D 9 11 Hs. 420830 HIF3A 1 7 Hs. 642660 C10orfl116 9 11 Hs. 511265 SEMA6D 1 7 Hs. 495912 DMD 9 11 Hs. 436657 CLU 9 12 Hs. 503126 SHANK2 4 8 Hs. 78482 PALM 6 10 Hs. 481342 SORBS2 4 8 Hs. 82318 WASF3 6 10 Hs. 169441 MAGI1 6 9 Hs. 268869 ADHFE1 5 Hs. 75652 GSTM5 8 10 Hs. 34494 AGXT2 5 Hs. 405156 PPAP28 8 10 Hs. 249129 CIDEA 5 Hs. 271771 SNCA 8 10 Hs. 302754 EFCBP1 5 Hs. 181855 CASC5 5 Hs. 521953 EFHC2 5 Hs. 506458 ANKS1B 1 6 Hs. 200100 Ells1 5 Hs. 445885 KIAA1217 1 6 Hs. 479703 FL21511 5 Hs. 643583 DKFZp667G2110 3 7 Hs.. 500750 HPSE2 5 Hs. 406787 FBX03 3 7 Hs. 380929 LDHD 5 Hs. 431498 FOXP1 3 7 All these genes are significantly consistently down-regulated (P < 10⁻⁵) in a large majority of cancer types. doi: 10.1371/journal.pone.0001149.t002

TABLE 6 Commonly Upregulated Genes in Pancreatic Cancer Gene Accession Symbol Gene Name FC NM_006475 POSTN periostin, osteoblast specific factor 13.28 NM_005980 S100P S100 calcium binding protein P 12.36 NM 004385 CSPG2 chondroitin sulfate proteoglycan 2 (versican) 10.57 NM 003118 SPARC secreted protein, acidic cysteine-rich (osteonectin) 10.46 NM 003225 TFF1 trefoil factor 1 (breast cancer, estrogen-inducible sequence 8.13 expressed in) NM 002026 FN1 fibronectin 1 7.93 NM 006142 SFN stratifin 7.81 NM 000393 COL5A2 collagen, type V, alpha 2 7.22 NM 005940 MMP11 matrix metalloproteinase 11 (stromelysin 3) 7.17 NM 000088 COL1A1 collagen, type I, alpha 1 6.50 NM 000930 PLAT plasminogen activator, tissue 6.46 NM 003064 SLPI secretory leukocyte protease inhibitor (antileukoproteinase) 6.01 NM 006516 SLC2A1 solute carrier family 2 (facilitated glucose transporter), member 1 5.39 NM 003226 TFF3 trefoil factor 3 (intestinal) 5.28 NM 004460 FAP fibroblast activation protein alpha 5.20 NM 003467 CXCR4 chemokine (C-X-C motif) receptor 4 5.18 NM 003247 THBS2 thrombospondin 2 5.04 NM 012101 TRIM29 tripartite motif-containing 4.91 NM 033664 CDH11 cadherin 11, type 2, OB-cadherin (osteoblast) 4.52 NM 006169 NNMT nicotinamide N-methyltransferase 4.51 NM 004425 ECM1 extracellular matrix protein 1 4.39 NM 003358 UGCG UDP-glucose ceramide glucosyltransferase 4.36 NM 000700 ANXA1 annexin A1 4.31 NM 004772 C5orf13 chromosome 5 open reading frame 13 4.29 NM 182470 PKM2 pyruvate kinase, muscle 4.28 NM 004994 MMP9 matrix metalloproteinase 9 (gelatinase B, 92 kDa gelatinase, 4.19 92 kDa type IV collagenase) NM 006868 RAB31 RAB31, member RAS oncogene family 4.18 NM 001932 MPP3 membrane protein, palmitoylated 3 (MAGUK p55 subfamily member 3) 4.16 AF200348 D2S448 Melanoma associated gene 4.14 NM 000574 DAF decay accelerating factor for complement (CD55, Cromer blood 4.11 group system) NM 000213 ITGB4 integrin beta 4.11 NM 001645 APOC1 apolipoprotein C-I 3.86 NM 198129 LAMA3 laminin, alpha 3 3.86 NM 002997 SDC1 syndecan 1 3.80 NM 001769 CD9 CD9 antigen (p24) 3.78 BC004376 ANXA8 annexim A8 3.74 NM 005620 S100A11 S100 calcium binding protein A11 (calgizzarin) 3.72 NM 002659 PLAUR plasminogen activator urokinase receptor 3.70 NM 002966 S100A10 S100 calcium binding protein A10 (annexin II ligand, calpactin I, 3.67 light polypeptide (p11)) NM 004898 CLOCK clock homolog (mouse) 3.65 NM 002345 LUM lumican 3.59 NM 006097 MYL9 myosin light polypeptide 9, regulatory 3.44 NM 004120 GBP2 guanylate binding protein 2, interferon-inducible 3.44 AK056875 LOC91316 similar to bK246H3.1 (immunoglobulin lambda-like polypeptide 3.40 1, pre-B-cell specific) NM 001827 CKS2 CDC28 protein kinase requlatorv subunit 2 3.36 NM 002203 ITGA2 integrin alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor) 3.35 NM 000599 IGFBP5 insulin-like growth factor binding protein 5 3.33 NM 004530 MMP2 matrix metalloproteinase 2 (gelatinase A, 72 kDa gelatinase, 3.33 72 kDa type IV collagenase) NM 004335 BST2 bone marrow stromal cell antigen 3.30 NM 000593 TAP1 transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) 3.29 NM 004915 ABCG1 ATP-bindina cassette sub-familv G (W

ITE), member 3.27 NM 001235 SERPINH 1 serine (or cysteine) proteinase inhibitor, clade H (heat shock 3.25 protein 47), member 1 (collagen binding protein 1) NM 001165 BIRC3 baculoviral IAP repeat-containing 3 3.23 NM 002658 PLAU plasminogen activator, urokinase 3.20 NM 021103 TMSB10 thymosin, beta 10 3.18 NM 000304 PMP22 peripheral myelin protein 22 3.15 XM 371541 K1AA1641 KIAA1641 protein 3.11 NM 012329 MMD monocyte to macrophage differentiation-associated 3.07 NM 182744 NBL1 neuroblastoma suppression of tumorigenicity 1 3.06 NM 002245 KCNK1 potassium channel, subfamily K, member 1 3.03 NM 000627 LTBP1 latent transforming growth factor beta binding protein 1 3.02 NM 000063 C2 complement component 2 3.01 NM 000100 CSTB cystatin B (stefin B) 2.99 NM 000396 CTSK cathepsin K (pycnodysostosis) 2.98 NM 016816 OAS1 2′ 5′-oliaoadenylate synthetase 1, 40/46 kDa 2.98 NM 004240 TRIP10 thyroid hormone receptor interactor 10 2.95 NM 000138 FBN1 fibrillin 1 (Marfan syndrome) 2.94 NM 002318 LOXL2 lysyl oxidase-like 2 2.92 NM 002053 GBP1 guanylate binding orotein 1 interferon-inducible, lysyl 67 kDa 2.90 NM 005564 LCN2 lipocalin 2 (oncogene 24p3) 2.88 NM 153490 KRT13 keratin 13 2.85 NM 004723 AR

GEF 2 rho/rac guanine nucleotide exchange factor (GEF) 2 2.80 NM 004146 NDUFB7 NADH dehydrozenase (ubiquinone) 1 beta subcomplex, 7, 18 kDa 2.79 NM 003937 KYNU kynureninase (L-kynurenine hvdrolase) 2.77 NM 002574 PRDX1 Peroxiredoxin 1 2.77 NM 002444 MSN moesin 2.73 NM 002901 RCN1 reticulocalbin 1, EF-hand calcium binding domain 2.73 NM 005165 ALDOC aldolase C, fructose-bisphosphate 2.72 NM 002204 ITGA3 integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor) 2.72 NM 033138 CALD1 caldesmon 1 2.71 NM 003816 ADAM9 a disintegrin and metalloproteinase domain 9 (meltrin gamma) 2.69 NM 173843 IL1RN interleukin 1 receptor antagonist 2.66 NM 000602 SERPINE 1 serine (or cysteine) proteinase inhibitor, clade E (nexin, 2.65 plasminggen activator inhibitor type 1), member 1 NM 002213 ITGB5 integrin, beta 5 2.64 NM 004447 EPS8 epidermal growth factor receptor pathway substrate 8 2.64 NM 002928 RGS16 regulator of G-protein singalling 16 2.62 NM 001288 CLIC1 chloride intracellular channel 1 2.61 NM 015996 TAGLN transgelin 2.57 NM 002087 GRN granulin 2.55 NM 001183 ATP6AP1 ATPase, H+ transporting, lysosomal accessory protein 1 2.54 NM 001730 KLF5 Kruppel-like factor 5 (intestinal) 2.51 NM 003516 HIST2H2AA histone 2, H2aa 2.50 NM 014736 KIAA0101 KIAA0101 gene product 2.49 NM 002290 LAMA4 laminin, alpha 4 2.49 NM 001826 CKS1B CDC28 protein kinase reaulatory subunit 1B 2.48 NM 001814 CTSC cathepsin C 2.45 NM 176825 SULT1C1 sulfotransferase family cytosolic, 1C, member 1 2.43 NM 002862 PYGB phosphorylase, glycogen; brain 2.41 NM 000917 P4HA1 procollagen-proline, 2-oxoglutarate 4-dioxygenase 2.41 (proline 4-hydroxylase), alpha polypeptideI NM 001428 EN01 enolase 1 (alpha) 2.40 NM 001425 EMP3 epithelial membrane protein 3 2.40 NM 019111 HLA-DRA maior histocompatibility complex, class II, DR alpha 2.38 NM 001387 DPYSL3 dihydropyrimidinase-like 3 2.36 NM 006471 MRCL3 myosin regulatory light chain MRCL3 2.34 NM 006332 IFI30 interferon gamma-inducible protein 30 2.34 NM 001312 CRIP2 cysteine-rich protein 2 2.33 NM 002224 ITPR3 inositol 1 4 5-triphosphate receptor tvpe 3 2.31 NM 053025 MYLK myosin light peptide kinase 2.29 NM 002785 PSG11 pregnancy specific beta-1-glycoprotein 11 2.27 NM 000900 MGP matrix Gla protein 2.26 NM 000962 PTGS1 prostaglandin-endoperoxide synthase 1 (prostaglandin G/H 2.25 synthase and cyclooxyenase) NM 005915 MCM6 minichromosome maintenance deficient 6 (MIS5 homolog, 2.24 S. pombe) (S. cerevisiae) NM 001067 TOP2A topoisomerase (DNA) II alpha 170 kDa 2.23 NM 001878 CRABP2 cellular retinoic acid binding protein 2 2.23 NM 006745 SC4MOL sterol-C4-methyl oxidase-like 2.22 NM 003528 HIST2H2 histone 2, H2be 2.22 BF347579 Transcribed sequence with strong similarity to protein pir: 2.21 I38500 (H. sapiens) I38500 interferon gamma receptor accessory factor-1 precursor - human NM 005261 GEM GTP binding protein overexpressed in skeletal muscle 2.19 NM 021874 CDC25B cell division cycle 25B 2.18 NM 022550 XRCC4 X-ray repair complementing defective repair in Chinese hamster 2.17 cells 4 NM 020250 GSN gelsolin (amyloidosis, Finnish type) 2.17 NM 002916 RFC4 replication factor C (activator 1) 4, 37 kDa 2.16 NM 005606 LGMN legumain 2.14 NM 006762 LAPTM5 Lysosomal-associated multispanning membrane protein-5 2.14 NM 002727 PRG1 proteoglycan 1, secretory granule 2.14 NM 002609 PDGFRB platelet-derived growth factor receptor, beta polypeptide 2.14 NM 001424 EMP2 epithelial membrane protein 2 2.12 NM_005022 PFN1 profilin 1 2.12 NM_001657 AREG amphiregulin amphireaulin (schwannoma-derived growth factor) 2.11 NM_005100 AKAP12 A kinase (PRKA) anchor protein (gravin) 12 2.11 NM_000860 HPGD hydroxyprostaglandin dehydrogenase 15 (NAD) 2.10 NM_007115 TNFAIP6 tumor necrosis factor alpha-induced protein 6 2.09 NM_021638 AFAP actin filament associated protein 2.08 NM_001946 DUSP6 dual specificity phosphatase 6 2.05 NM_181802 UBE2C ubiquitin-conjugating enzyme E2C 2.04 NM_002593 PCOLCE procollagen C-endopeptidase enhancer 2.02 NM_033292 CASP1 caspase 1, apoptosis-related cysteine protease 2.02 (interleukin 1, beta, convertase) NM_003870 IQGAP1 IQ motif containing GTPase activating protein 1 2.02 NM_005563 STMN1 stathmin 1/oncoprotein 18 2.01 NM_005558 LAD1 ladinin 1 2.01 NM_001776 ENTPD1 ectonucleoside triphosphate diphosphohydrolase 1 2.00 NM_001299 CNN1 calponin 1, basic, smooth muscle 2.00 AK055128 PSMD14 proteasome (prosome, macropain) 26S subunit, non-ATPase, 14 2.00 NM_006304 SHFM1 split hand/foot malformation (ectrodactyly) type 1 1.98 NM_004024 ATF3 activating transcription factor 3 1.98 NM_000291 PGK1 phosphoglycerate kinase 1 1.98 NM_006520 TCTE1L t-complex-associated-testis-expressed 1-like 1.97 NM_201380 PLEC1 plectin 1 intermediate filament binding protein 500 kDa 1.97 NM_002838 PTPRC protein tyrosine phosphatase, receptor type, C 1.97 NM_000211 ITGB2 integrin, beta 2 (antigen CD18 (p95), lymphocyte function- 1.97 associated antigen 1; macrophage antigen 1 (mac-1) beta subunit) NM_002577 PAK2 p21 (CDKN1A)-activated kinase 2 1.96 NM_000295 SERPINA 1 serine (or cysteine) proteinase inhibitor, clade A 1.96 (alpha-1 antiproteinase, antitrypsin), member 1 NM_183001 SHC1 SHC (Src homotogy 2 domain containing) transforming protein 1 1.96 NM_005019 PDE1A phosphodiesterase 1A, calmodulin-dependent 1.95 NM_002298 LCP1 lymphocyte cytosolic protein 1 (L-plastin) 1.95 NM_006769 LMO4 LIM domain only 4 1.94 NM_001465 FYB FYN binding protein (FYB-120/130) 1.93 NM_183422 TSC22 transforming growth factor beta-stimulated protein TSC-22 1.92 NM_001777 CD47 CD47 antigen (Rh-related antigen, integrin-associated signal 1.92 transducer) NM_001755 CBFB core-binding factor, beta subunit 1.90 NM_005544 IRS1 insulin receptor substrate 1 1.88 NM_000698 ALOX5 arachidonate 5-lipoxygenase 1.88 NM_006096 NDRG1 N-myc downstream regulated gene 1 1.88 NM_001105 ACVR1 activin A receptor, type 1 1.87 NM_003105 SORL1 sortilin-related receptor, L(DLR class) A repeats-containing 1.85 NM_001998 FBLN2 fibulin 2 1.85 NM_014791 MELK maternal embryonic leucine zipper kinase 1.85 NM_003092 SNRPB2 small nuclear ribonucleoprotein polypeptide B 1.84 NM_001120 TETRAN tetracycline transporter-like protein 1.84 NM_182943 PLOD2 procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1.83 (lysine hydroxylase) 2 NM_181862 BAC

brain acyl-CoA hydrolase 1.82 NM_021102 SPINT2 serine protease inhibitor, Kunitz type, 2 1.82 NM_004419 DUSP5 dual specificity phosphatase 5 1.81 NM_006482 DYRK2 dual specificity tyrosine-(Y)-phosphorylation regulated 1.81 kinase 2 NM_145690 YWHAZ tyrosine 3-monooxygenase/tryptophan 5-monooxygenase 1.81 activation protein, zeta polypeptide NM_000714 BZRP benzodiazapine receptor (peripheral) 1.81 NM_013995 LAMP2 lysosomal-associated membrane protein 2 1.80 CA450153 ACYP1 acylphosphatase 1, erythrocyte (common) type 1.80 NM_000405 GM2A GM2 ganglioside activator protein 1.79 NM_139275 AKAP1 A kinase (PRKA) anchor protein 1 1.79 NM_001679 ATP1B3 ATPase, Na+/K+ transporting, beta 3 polypeptide 1.79 NM_016343 CENPF centromere protein F, 350/400 ka (mitosin) 1.79 NM_002201 ISG20 interferon stimulated gene 20 kDa 1.79 NM_002463 MX2 myxovirus (influenza virus) resistance 2 (mouse) 1.79 NM_006820 C1orf29 chromosome 1 open reading frame 29 1.79 NM_201397 GPX1 glutathione peroxidase 1 1.79 NM_005738 ARL4 ADP-ribosylation factor-like 4 1.78 NM_001038 SCNN1A sodium channel nonvoltage-gated 1 alpha 1.78 NM_002863 PYGL phosphorylase, glycogen; liver (Hers disease, glycogen 1.78 storage disease type VI) NM_001281 CKAP1 cytoskeleton associated protein 1 1.77 NM_003879 CFLAR CASP8 and FADD-like apoptosis regulator 1.76 NM_182948 PRKACB protein kinase, cAMP-dependent catalytic, beta 1.75 NM_006009 TUBA3 tubulin, alpha 3 1.75 NM_201444 DGKA diacylglycerol kinase, alpha 80 kDa 1.74 NM_005471 GNPDA1 glucosamine-6-phosphate deaminase 1 1.74 NM_001451 FOXF1 forkhead box F1 1.74 NM_001988 EVPL envoplakin 1.73 NM_021724 NR1D1 nuclear receptor subfamily 1, group D member 1 1.73 NM_006364 SEC23A Sec23 homolog A (S. cerevisiae) 1.72 NM_002129 HMGB2 high-mobility group box 2 1.72 NM_004172 SLC1A3 solute carrier family 1 (glial high affinity glutamate 1.71 transporter), member 3 NM_001421 ELF4 E74-like factor 4 (ets domain transcription factor) 1.71 NM_005566 LD

A lactate dehydrogenase A 1.70 NM_000270 NP nucleoside phosphorylase 1.69 NM_153425 TRADD TNFRSF1A-associated via death domain 1.67 NM_004762 PSCD1 pleckstrin homology, Sec7 and coiled-coil domains 1.67 (cytohesin 1) NM_001985 ETFB electron-transfer-flavoprotein, beta polypeptide 1.67 NM_016587 CBX3 chromobox homolog 3 (HP1 gamma homolog, Drosophila) 1.66 NM_002085 GPX4 glutathione peroxidase 4 (phospholipid hydroperoxidase) 1.66 NM_002795 PSMB3 proteasome (prosome, macropain) subunit, beta type, 3 1.65 NM_000963 PTGS2 prostaglandin-endoperoxide synthase 2 (prostaglandin G/H 1.65 synthase and cyclopxyoenase) NM_001642 APLP2 amyloid beta (A4) precursor-like protein 2 1.65 NM_000569 FCGR3A Fc fragment of lgG low affinity iiia receptor for (CD16) 1.64 NM_000362 TIMP3 tissue inhibitor of metalloproteinase 3 (Sorsby fundus 1.63 dystrophy, pseudoinflammatory) NM_002417 MKI67 antigen identified by monoclonal antibody Ki-67 1.63 NM_000175 GPI glucose phosophate isomerase 1.63 AF179995 SEPT8 septin 8 1.62 NM_004121 GGTLA1 gamma-glutamyltransferase-like activity 1 1.62 NM_002690 POLB polymerase (DNA directed), beta 1.62 NM_004334 BST1 bone marrow stromal cell antigen 1 1.61 NM_001892 CSNK1A1 casein kinase 1, alpha 1 1.61 NM_014670 BZW1 basic leucine zipper and W2 domains 1 1.60 NM_001110 ADAM10 a disintegrin and metalloproteinase domain 10 1.60 NM_005792 MPHOSP H6 M-phase phosphoprotein 6 1.60 NM_001126 ADSS adenylosuccinate synthase 1.59 XM 376059 SERTAD2 SERTA domain containing 2 1.59 NM_001664 ARHA ras homolog gene family, member A 1.59 NM_002475 MLC1SA myosin light chain 1 slow a 1.59 NM_014498 GOLPH4 golgi phosphoprotein 4 1.59 NM_005964 MYH10 myosin heavy polypeptide 10 non-muscle 1.59 NM_003330 TXNRD1 thioredoxin reductase 1 1.59 NM_001757 CBR1 carbonyl reductase 1 1.58 NM_003130 SRI sorcin 1.57 NM_006765 TUSC3 tumor suppressor candidate 3 1.57 NM_183047 PRKCBP 1 protein kinase C binding protein 1 1.57 NM_005333 HCCS holocytochrome c synthase (cytochrome c heme-lyase) 1.57 NM_001444 FABP5 fatty acid binding protein 5 (psoriasis-associated) 1.57 NM_001799 CDK7 cyclin-dependent kinase 7 (M015 homolog, Xenopus laevis, 1.57 cdk-activating kinase) NM_001539 DNAJA1 DnaJ (Hsp40) homolog subfamily A member 1 1.57 NM_004475 FLOT2 flotillin 2 1.57 NM_004308 ARHGAP 1 Rho GTPase activating protein 1 1.56 NM_002388 MCM3 MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) 1.56 NM_006435 IFITM2 interferon induced transmembrane protein 2 (1-8D) 1.56 NM_000454 SOD1 superoxide dismutase 1, soluble (amyotrophic lateral 1.56 sclerosis 1 (adult)) NM_015161 ARL6IP ADP-ribosylation factor-like 6 interacting protein 1.56 NM_078480 SIA

BP1 fuse-binding protein-interacting represser 1.56 NM_025207 PP591 FAD-synthetase 1.56 NM_002833 PTPN9 protein tyrosine phosphatase non-receptor type 9 1.55 NM_001753 CAV1 caveolin 1 caveolae protein 22 kDa 1.55 NM_003286 TOP1 topoisomerase (DNA) I 1.55 BU739663 Transcribed sequence with moderate similarity to protein 1.55 sp: P13196 (H. sapiens) HEM1_HUMAN 5-aminolevulinic acid synthase, nonspecific mitochondrial precursor NM_006788 RALBP1 ralA binding protein 1 1.54 NM_000944 PPP3CA protein phosphatase 3 (formerly 2B), catalytic subunit, alpha 1.54 isoform (calcineurin A alpha) NM_003374 VDAC1 voltaqe-dependent anion channel 1 1.54 NM_000560 CD53 CD53 antigen 1.54 NM_002037 FYN FYN oncogene related to SRC FGR, YES 1.54 NM_002885 RAP1GA1 RAP1 GTPase activating protein 1 1.53 NM_018979 PRKWNK 1 lprotein kinase, lysine deficient 1 1.53 NM_002835 PTPN12 protein tyrosine phosphatase, non-receptor type 12 1.53 NM_007315 STAT1 signal transducer and activator of transcription 1, 91 kDa 1.52 NM_014846 KIAA0196 KIAA0196 gene product 1.52 NM_001237 CCNA2 cyclin A2 1.52 NM_004596 SNRPA small nuclear ribonucleoprotein polypeptide A 1.52 NM_002790 PSMA5 proteasome (prosome, macropoain) subunit, alpha type, 5 1.52 NM_015361 R3HDM R3H domain (binds single-stranded nucleic acids) containing 1.52 NM_001665 ARHG ras homolog gene family, member G (rho G) 1.51 NM_002788 PSMA3 proteasome (prosome macropain) subunit, alpha type, 3 1.50 NM_006904 PRKDC protein kinase, DNA-activated, catalytic polypeptide 1.50 NM_003400 XPO1 exportin 1 (CRM1 homolog, yeast) 1.50 NM_178014 OK/SW-cl.56 beta 5-tubulin 1.50 NM_002634 PHB prohibitin 1.49 NM_004792 PPIG peptidyl-prolyl isomerase G (cyclophilin G) 1.49 MM_002508 NID nidogen (enactin) 1.49 NM_001765 CD1C CD1C antigen, c polypeptide 1.48 NM_000311 PRNP prion protein (p27-30) (Creutzfeld-Jakob disease, Gerstmann- 1.48 Strausler-Scheinker syndrome, fatal familial insomnia) NM_006437 ADPRTL1 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 1.48 NM_002759 PRKR protein kinase, interferon-inducible double stranded RNA dependent 1.48 NM_014669 KIAA0095 KIAA0095 gene product 1.47 NM_003391 WNT2 wingless-type MMTV integration site family member 2 1.47 NM_004309 ARHGDIA Rho GDP dissociation inhibitor (GDI) alpha 1.47 NM_000418 IL4R interleukin 4 receptor 1.46 NM_003352 UBL1 ubiquitin-like 1 (sentrin) 1.46 NM_006290 TNFAIP3 tumor necrosis factor alpha-induced protein 3 1.45 NM_004763 ITGB1BP1 integrin beta 1 binding protein 1 1.45 NM_005754 G3BP Ras-GTPase-activating protein SH3-domain-binding protein 1.45 NM_021990 GABRE gamma-aminobutyric acid (GABA) A receptor, epsilon 1.44 NM_001379 DNMT1 DNA (cytosine-5-)-methyltransferase 1 1.44 NM_001154 ANXA5 annexin A5 1.44 NM_004354 CCNG2 cyclin G2 1.44 NM_005002 NDUFA9 NADH dehydroaenase (ubiquinone) 1 alpha subcomplex, 9, 39 kDa 1.43 NM_001931 DLAT dihydrolipoamide S-acetyltransferase (E2 component of pyruvate 1.43 dehydroaenase complex) NM_005902 MADH3 MAD mothers against decapentaplegic homolog 3 (Drosophila) 1.43 NM_000110 DPYD dihydropyrimidine dehydrogenase 1.43 NM_001316 CSE1L CSE1 chromosome segregation 1-like (yeast) 1.43 NM_000167 GK glycerol kinase 1.43 NM_001924 GADD45 A growth arrest and DNA-damage-inducible, alpha 1.42 NM_014225 PPP2R1A protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), 1.42 alpha isoform NM_001233 CAV2 caveolin 2 1.42 NM_176863 PSME3 proteasome (prosome, macropain) activator subunit 3 (PA28 gamma; Ki) 1.42 NM_001905 CTPS CTP synthase 1.41 NM_005653 TFCP2 transcription factor CP2 1.41 NM_003405 YWHAH tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation 1.41 protein, eta polypeptide NM_003392 WNT5A wingless-type MMTV integration site family, member 5A 1.40 NM_002375 MAP4 microtubule-associated protein 4 1.40 NM_006353 HMGN4 high mobility group nucleosomal binding domain 4 1.39 NM_006527 SLBP stem-loop (histone) bindino protein 1.39 NM_000517 HBA2 hemoglobin alpha 2 1.38 NM_002661 PLCG2 phospholipase C, gamma 2 (phosphatidylinositol-specific) 1.38 NM_001493 GDI1 GDP dissociation inhibitor 1 1.38 NM_181430 FOXK2 forkhead box K2 1.38 NM_002086 GRB2 growth factor receptor-bound protein 2 1.38 NM_002868 RAB5B RAB5B, member RAS oncogene family 1.37 NM_002768 PCOLN3 procollagen (type III) N-endopeptidase 1.37 NM_014742 TM9SF4 transmembrane 9 superfamily protein member 4 1.37 NM_004344 CETN2 centrin, EF-hand protein, 2 1.37 NM_002881 RALB v-ral simian leukemia viral oncogene homolog B 1.36 (ras related; GTP binding protein) NM_004099 STOM stomatin 1.36 NM_031844 HNRPU heterogeneous nuclear ribonucleoprotein U 1.36 (scaffold attachment factor A) NM_000480 AMPD3 adenosine monophosphate deaminase (isoform E) 1.35 NM_006561 CUGBP2 CUG triplet repeat RNA binding protein 2 1.35 NM_152879 DGKD diacylglycerol kinase delta 130 kDa 1.35 NM_138558 PPP1R8 protein phosphatase 1 reQulatory (inhibitor) subunit 8 1.35 NM_004941 DHX8 DEAH (Asp-Glu-Ala-His) box polypeptide 8 1.34 NM_021079 NMT1 N-myristoyltransferase 1 1.33 NM_004622 TSN translin 1.33 NM_002473 MYH9 myosin, heavy polypeptide 9, non-muscle 1.33 NM_006889 CD86 CD86 antigen (CD28 antigen ligand 2, B7-2 antigen) 1.33 NM_004383 CSK c-src tyrosine kinase 1.33 NM_004317 ASNA1 arsA arsenite transoorter ATP-binding homolog 1 1.33 (bacterial) NM_024298 LENG4 leukocyte receptor cluster (LRC) member 4 1.32 NM_001912 CTSL cathepsin L 1.32 NM_001357 DHX9 DEAH (Asp-Glu-Ala-His) box polypeptide 9 1.32 NM_006849 PDIP protein disulfide isomerase, pancreatic 1.32 NM_018457 DKFZP564J157 DKFZ, 0564J157 protein 1.31 NM_024880 TCF7L2 transcription factor 7-like 2 (T-cell specific, HMG-box) 1.31 NM_002081 GPC1 glypican 1 1.31 NM_004235 KLF4 Kruppel-like factor 4 (gut) 1.31 NM_005565 LCP2 lymphocyte cytosolic protein 2 (S

2 domain containing 1.30 leukocyte protein of 76 kDa) NM_002667 PLN phospholamban 1.30 NM_004946 DOCK2 dedicator of cytokinesis 2 1.30 NM_002035 FVT1 follicular lymphoma variant translocation 1 1.29 NM_002865 RAB2 RAB2 member RAS oncogene family 1.29 NM_002806 PSMC6 proteasome (prosome macropain) 26S subunit ATPase 6 1.29 NM_004240 TRIP10 thyroid hormone receptor interactor 10 1.28 NM_003760 EIF4G3 eukaryotic translation initiation factor 4 gamma, 3 1.28 NM_005151 USP14 ubiquitin specific protease 14 (

RNA quanine 1.28 transglycosylase) NM_015922 H105E3 NAD(P) deoendent steroid dehydropenase-like 1.27 NM_033306 CASP4 caspase 4 apoptosis-related cysteine protease 1.27 NM_198189 COPS8 COP9 constitutive photomorphogenic homolog subunit 1.27 8 (Arabidopsis) NM_001933 DLST dihydrolipoamide S-succinyltransferase (E2 component 1.27 of 2-oxo-qlutarate complex) NM_015004 KlAA0116 KlAA0116 protein 1.27 NM_033362 MRPS12 mitochondrial ribosomal protein S12 1.27 NM_004180 TANK TRAF family member-associated NFKB activator 1.26 NM_014734 KlAA0247 KlAA0247 1.26 NM_005271 GLUD1 glutamate dehydropenase 1 1.25 NM_003009 SEPW1 selenoprotein W, 1 1.25 NM_182641 FALZ fetal Alzheimer antigen 1.24 NM_007362 NCBP2 nuclear cap binding protein subunit 2 20 kDa 1.24 NM_004292 RIN1 Ras and Rab interactor 1 1.24 NM_014608 CYFIP1 cytoplasmic FMR1 interacting protein 1 1.23 NM_022333 TIAL1 TIA1 cytotoxic oranule-associated RNA binding protein-like 1 1.23 NM_003126 SPTA1 spectrin alpha erythrocytic 1 (elliptocytosis 2) 1.22 NM_014602 PIK3R4 phosphoinositide-3-kinase regulatory subunit 4, p150 1.18 NM_002194 INPP1 inositol polyphosphate-1-phosphatase 1.16 Note: Accession IDs “NM_XXXX” are uniquely assigned to each gene by National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/sites/entrez?db=nuccore).

indicates data missing or illegible when filed

TABLE 7 Commonly Downregulated Genes in Pancreatic Cancer Gene Accession Symbol Gene Name FC NM_006499 LGALS8 galoctosite-binding, soluble, 8 (galectin 8) 0.87 NM_000466 PEX1 peroxisome biogenesis factor 1 0.81 NM_002766 PRPSAP1 phosphoribosyl pyrophosphate synthetase-associated protein 1 0.81 NM_147131 GALT galactose-1-phosphate uridylyltransferase 0.80 NM_002101 GYPC glycophorin C (Gerbich blood group) 0.80 NM_002880 RAF1 v-raf-1 murine leukemia viral oncogene homolog 1 0.80 NM_004649 C218rf33 chromosome 21 open reading frame 33 0.80 NM_003262 TLOC1 translocation protein 1 0.79 NM_147223 NCOA1 nuclear receptor coactivator 1 0.79 NM_007062 PWP1 nuclear phosphoprotein similar to S. cerevisiae PWP1 0.79 NM_005561 LAMP1 lysosomal-associated membrane protein 1 0.79 NM_006810 PDIR for protein disulfide isomerase-related 0.78 NM_033360 KRAS2 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog 0.77 NM_001513 GSTZ1 glutathione transferase zeta 1 (maleylacetoacetate isomerase) 0.77 NM_006184 NUCB1 nucleobindin 1 0.77 NM_001634 AMD1 adenosylmethionine decarboxylase 1 0.76 NM_006749 SLC20A2 solute carrier family 20 (phosphate transporter), member 2 0.76 NM_003144 SSR1 signal sequence receptor alpha (translocon-associated protein alpha) 0.76 NM_004606 TAF1 TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated 0.75 factor 250 kDa BX648788 MRNA; cDNA DKFZP686M12165 (from clone DKFZP686M12165) 0.75 NM_004035 ACOX1 acyl-Coenzyme A oxidase 1 palmitoyl 0.74 NM_000287 PEX6 peroxisomal biogenesis factor 6 0.73 NM_003884 PCAF p300/CBP-associated factor 0.73 NM_006870 DSTN destrin (actin depolymerizing factor) 0.73 NM_001604 PAX6 paired box gene 6 (aniridia keratitis) 0.72 NM_000722 CACNA2 D1 calcium channel voltage-dependent alpha 2/delta subunit 1 0.72 NM_033022 RPS24 ribosomal protein S24 0.72 NM_004563 PCK2 phosphoenolpyruvate carboxykinase 2 (mitochondrial) 0.72 NM_002602 PDE6G phosphodiesterase 6G cGMP-specific, rod, gamma 0.72 NM_001889 CRYZ crystalline, zeta (quinone reductase) 0.72 NM_002339 LSP1 lymphocyte-specific protein 1 0.72 NM_016848 SHC3 src homology 2 domain containing transforming protein C3 0.71 NM_002906 RDX radixin 0.71 NM_007014 WWP2 Nedd-4-like ubiquitin-protein ligase 0.71 NM_000414 HSD17B4 hydroxysteroid (17-beta) dehydrogenase 4 0.71 NM_001127 AP1B1 adaptor-related protein complex 1, beta 1 subunit 0.71 NM_002402 MEST mesoderm specific transcript homolog (mouse) 0.70 NM_033251 RPL13 ribosomal protein L13 0.70 NM_139069 MAPK9 mitogen-activated protein kinase 9 0.70 NM_002913 RFC1 replication factor C (activator 1) 1, 145 kDa 0.70 NM_000487 ARSA arvlsulfatase A 0.70 NM_006973 ZNF32 zinc finger protein 32 (KOX 30) 0.70 NM_005310 GRB7 growth factor receptor-bound protein 7 0.70 NM_005962 MXl1 MAX interacting protein 1 0.69 NM_005359 MADH4 MAD, mothers against decapentaplegic homolog 4 (Drosophila) 0.69 NM_002340 LSS lanosterol synthase (2 3-oxidosqualene-lanosterol cyclase) 0.69 NM_003684 MKNK1 MAP kinase-interacting serine/threonine kinase 1 0.68 NM_005671 D8S2298 E reproduction 8 0.68 NM_000309 PPOX protoporphyrinogen oxidase 0.68 NM_000994 RPL32 ribosomal protein L32 0.68 NM_000972 RPL7A ribosomal protein L7a 0.68 NM_005101 G1P2 interferon, alpha-inducible protein (clone IFI-15K) 0.67 NM_001129 AEBP1 AE binding protein 1 0.67 NM_001011 RPS7 ribosomal protein S7 0.67 NM_001153 ANXA4 annexin A4 0.67 NM_012335 MY01F myosin IF 0.66 NM_005007 NFKBIL1 nuclear factor of kappa light polypeptide gene enhancer in 0.66 B-cells inhibitor-like 1 NM_001870 CPA3 carboxypeptidase A3 (mast cell) 0.66 NM_181826 NF2 neurofibromin 2 (bilateral acoustic neuroma) 0.66 NM_000285 PEPD peptidase D 0.66 NM_006180 NTRK2 neurotrophic tyrosine kinase, receptor type 2 0.66 NM_000543 SMPD1 sphingomyelin phosphodiesterase 1, acid lysosomal 0.66 (acid sphinagmyelinase) NM_001459 FLT3LG fms-related tyrosine kinase 3 ligand 0.65 NM_003750 EIF3S10 eukaryotic translation initiation factor 3, subunit 10 theta, 0.65 150/170 kDa NM_005570 LMAN1 lectin mannose-binding, 1 0.65 NM_004409 DMPK dystrophia myotonica-protein kinase 0.65 NM_172159 KCNAB1 potassium voltage-gated channel, shaker-related subfamily, 0.65 beta member 1 XM 352750 COL14A1 collagen, type XIV, alpha 1 (undulin) 0.65 NM_001731 BTG1 B-cell translocation gene 1, anti-proliferative 0.65 NM_000884 IMPDH2 IMP (inosine monophosphate) dehydrogenase 2 0.64 NM_001885 CRYAB crystallin, alpha B 0.64 NM_000240 MAOA monoamine oxidase A 0.64 NM_003136 SRP54 siqnal recognition particle 54 kDa 0.63 NM_000281 PCBD 6-pyruvoyl-tetrahydropterin synthase/dimerization cofactor of 0.63 hepatocyte nuclear factor 1 alpha (TCF1) NM_005729 PPIF peptidylprolpyl isomerase F (cyclophilin F) 0.63 NM_006481 TCF2 transcription factor 2, hepatic; LF-B3′ variant hepatic nuclear factor 0.63 NM_002089 CXCL2 chemokine (C-X-C motif) liqand 2 0.63 NM_001961 EEF2 eukaryotic translation elonqation factor 2 0.63 NM_001801 CDO1 cysteine dioxygenase type I 0.63 NM_006389 HYOU1 hypoxia up-regulated 1 0.63 XM 167711 ITGA8 integrin, alpha 8 0.62 NM_014765 TOMM20 translocase of outer mitochondrial membrane 20 homolog (yeast) 0.62 NM_006714 SMPDL3 A sphingomyelin phosphodiesterase, acid-like 3A 0.62 NM_000016 ACAOM acyl-Coenzyme A dehydrogenase C-4 to C-12 straiqht chain 0.62 NM_003924 PHOX2B paired-like homeobox 2b 0.62 NM_002078 GOLGA4 golgi autoantigen, golgin subfamily a 4 0.62 NM_002736 PRKAR2 B protein kinase cAMP-dependent, requlatory, type II beta 0.62 BQ217469 KlAA0114 KlAA0114 gene product 0.61 NM_006307 SRPX sushi-repeat-containing protein X-linked 0.61 NM_002184 IL6ST interleukin 6 siqnal transducer (gp130 oncostatin M receptor) 0.61 NM_153186 ANKR015 ankyrin repeat domain 15 0.61 NM_003038 SlC1A4 solute carrier family 1 (glutamate/neutral amino acid transporter), 0.60 member 4 NM_006195 PBX3 pre-B-cell leukemia transcription factor 3 0.60 NM_000327 ROM1 retinal outer segment membrane protein 1 0.60 NM_003463 PTP4A1 protein tyrosine phosphatase type IVA, member 1 0.60 NM_001520 GTF3C1 general transcription factor iiiC polypeptide 1 alpha 220 kDa 0.60 NM_006277 ITSN2 intersectin 2 0.59 NM_000985 RPL17 ribosomal protein L17 0.59 NM_000909 NPY1R neuropeptide Y receptor Y1 0.59 NM_001014 RPS10 ribosomal protein S10 0.59 NM_022307 ICA1 islet cell autoantigen 1 69 kDa 0.58 NM_002567 PBP prostatic binding protein 0.58 NM_012324 MAPK81P 2 mitogen-activated protein kinase 8 interacting protein 2 0.58 NM_004490 GRB14 growth factor receptor-bound protein 14 0.58 NM_004733 SLC33A1 solute carrier family 33 (acetyl-CoA transporter), member 1 0.57 NM_002197 AC01 aconitase 1, soluble 0.57 NM_000505 F12 coagulation factor Xii (Hageman factor) 0.57 NM_005010 NRCAM neuronal cell adhesion molecule 0.56 NM_006963 ZNF22 zinc finger protein 22 (KOX 15) 0.56 NM_006827 TMP21 transmembrane trafficking protein 0.55 NM_004394 DAP death-associated protein 0.54 NM_001089 ABCA3 ATP-binding cassette, sub-family A (ABC), member 3 0.54 NM_004470 FKBP2 FK506 binding protein 2, 13 kDa 0.53 NM_005749 TOB1 transducer of ERBB2, 1 0.53 NM_001355 DDT D-dopachrome tautomerase 0.53 NM_002111 HD huntington (Huntington disease) 0.53 NM_002635 SlC25A3 solute carrier family 25 (mitochondrial carrier; phosphate carrier), 0.53 member 3 NM_005596 NFIB nuclear factor I/B 0.53 NM_006273 CCL7 chemokine (C-C motif) liqand 7 0.53 NM_001013 RPS9 ribosomal protein S9 0.52 NM_001551 IGBP1 immunoglobulin (CD79A) binding protein 1 0.52 NM_004498 ONECUT 1 one cut domain, family member 1 0.52 NM_004484 GPC3 glypican 3 0.52 NM_130797 DPP6 dipeptidylpeptidase 6 0.52 NM_000746 CHRNA7 cholineragic receptor, nicotinic, alpha polypeptide 7 0.51 NM_001756 SERPINA 6 serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase 0.51 antitrypsin), member 6 NM_001327 CTAG1 cancer/testis antigen 1 0.51 NM_003651 CSDA cold shock domain protein A 0.50 NM_005848 IRLB c-myc promoter-binding protein 0.50 BC040073 H19 H19, imprinted maternally expressed untranslated mRNA 0.50 NM_002228 JUN v-jun sarcoma virus 17 oncogene homolog (avian) 0.49 NM_000795 DRD2 dopamine receptor D2 0.48 NM_002084 GPX3 glutathione peroxidase 3 (plasma) 0.48 NM_002716 PPP2R1B protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), 0.48 beta isoform NM_005166 APLP1 amyloid beta (A4) precursor-like protein 1 0.48 NM_005911 MAT2A methionine adenosyltransferase II, alpha 0.47 NM_000208 INSR insulin receptor 0.47 NM_170736 KCNJ15 potassium inwardly-rectifying channel, subfamily J, member 15 0.47 NM_001190 BCAT2 branched chain aminotransferase 2, mitochondrial 0.47 NM_005336

DLBP hiqh density lipoprotein binding protein (viqilin) 0.46 NM_001076 UGT2B15 UDP glycosyltransferase 2 family, polypeptide B15 0.46 NM_001152 SLC25A5 solute carrier family 25 (mitochondrial carrier; adenine nucleotide 0.46 translocator, member 5 NM_002729 HHEX hematopoietically expressed homeobox 0.46 NM_002847 PTPRN2 protein tyrosine phosphatase, receptor type, N polypeptide 2 0.44 NM_000447 PSEN2 presenilin 2 (Alzheimer disease 4) 0.44 NM_152868 KCNJ4 potassium inwardly-rectifying channel, subfamily J, member 4 0.44 NM_001759 CCND2 cyclin D2 0.44 NM_000316 PTHR1 parathyroid hormone receptor 1 0.44 NM_001612 ACRV1 acrosomal vesicle protein 1 0.43 NM_002467 MYC v-mc myelocytomatosis viral oncogene homolog (avian) 0.43 NM_004454 ETV5 ets variant gene 5 (ets-related molecule) 0.43 NM_002846 PTPRN protein tyrosine phosphatase, receptor type N 0.43 NM_005622 SAH SA hypertension-associated homolog (rat) 0.42 NM_001989 EVX1 eve, even-skipped homeo box homolog 1 (Drosophila) 0.42 NM_000166 GJB1 gap junction protein, beta 1, 32 kDa (connexin 32, Charcot-Marie- 0.42 Tooth neuropathy, X-linked) NM_014685 HERPUD 1 homocysteine-inducible, endoplasmic reticulum stress-inducible, 0.42 ubiquitin-like domain member 1 NM 001735 C5 complement component 5 0.41 NM 005504 BCAT1 branched chain aminotransferase 1, ctyosolic 0.41 NM 006808 SEC61B Sec61 beta subunit 0.40 NM 006751 SSFA02 sperm specific antigen 2 0.39 NM 005947 MT1B metallothionein 1B (functional) 0.38 NM 005576 LOXL1 lysyl oxidase-like 1 0.37 NM 005627 SGK serum/glucocorticoid regulated kinase 0.36 NM 004683 RGN regucalcin (senescence marker protein-30) 0.36 NM 00918 P4HB procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), 0.36 beta polypeptide (protein disulfide isomerase; thyroid hormone binding protein p55) BC044862 Macrophage stimulating 1 (hepatocyte growth factor-like), mRNA 0.35 (cDNA clone IMAGE: 4821945), with apparent retained intron NM 005952 MT1X metallothionein 1X 0.35 NM 000429 MAT1A methionine adenosyltransferase 1, alpha 0.35 NM 004010 DMD dystrophin (muscular dystrophy, Duchenne and Becker types) 0.34 NM 000689 ALDH1A1 aldehyde dehydrogenase 1 family, member A1 0.34 NM 002889 RARRES2 retinoic acid receptor responder (tazarotene induced) 2 0.33 NM 006280 SSRA signal sequence receptor, delta (translocon-associated protein delta) 0.33 NM 003819 PABPC4 poly(A) binding protein, cytoplasmic 4 (inducible form) 0.32 NM 000755 CRAT carnitine aceltyltransferase 0.32 NM 015684 ATP5S ATP synthase, H+ transporting, mitochondrial F0 complex, subunit s .030 (factor B) NM 033200 BC002942 hypothetical protein BC002942 0.30 BCG986717 Transcribed sequences 0.29 NM 148923 CYB5 cytochrome b-5 0.29 NM 000609 CXCL12 chemokine (C-X-C motif) ligand 12 (stromal cell-derived factor 1) 0.29 NM 001979 EPHX2 epoxide hydrolase 2, cytoplasmic 0.28 NM 001332 CTNND2 catenin (caherin-associated protein), delta 2 (neural plakophilin-related 0.27 arm-repeat protein) NM 001831 CLU clusterin (complement lysis inhibitor, SP-40, 40, sulfated glycoprotein 2, 0.27 testosterone-repressed prostate message 2, apolipoprotein J) NM 005080 XBP1 X-box binding protein 1 0.27 NM 000156 GAMT guanidinoacetate N-methyltransferase 0.27 NM 182848 CLDN10 claudin 10 0.26 NM 000065 C6 complement component 6 0.26 NM 000128 F11 coagulation factor XI (plasma thromboplasin antecedent) 0.24 NM 003822 MR5A2 nuclear receptor subfamily 5, group A, member 2 0.24 NM 006406 PRDX4 peroxiredoxin 4 0.21 BM799844 BNIP3 BCL2/adenovirus E1B 19 kDa interacting protein 3 0.21 NM 018646 TRPV6 transient receptor potential cation channel, subfamily V, member 6 0.21 NM 005013 NUCB2 nucleobindin 2 0.21 NM 000624 SERPINA 3 serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, 0.19 antitrypsin), member 3 NM 005065 SEL 1L sel-1 suppressor of lin-12-like (C. elegans) 0.18 NM 198235 RNASE 1 ribonuclease, RNase A family, 1 (pancreatic) 0.17 NM 006498 LGALS2 lectin, galactoside-binding, soluble, 2 (galectin 2) 0.16 NM 002899 RBP1 retinol binding protein 1, cellular 0.12 NM 004413 DPEP1 dipeptidase 1 (renal) 0.12 NM 021603 FXYD2 FXYD domain contaning ion transport regulator 2 0.09 NM 138938 PAP pancreatitis-associated protein 0.08 NM 201553 FGL fibrinogen-like 1 0.07 NM 001482 GATM glycerine amidinotransferase (L-arrginine: glycine amidinotransferase) 0.04 NM 033240 ELA2A elastase 2^(a) 0.02 NM 000101 CYBA cytochrome b-245, alpha polypeptide 0.02 Note: Accession IDs “NM_XXXX” are uniquely assigned to each gene by National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/sites/entrez?db=nuccore).

indicates data missing or illegible when filed

TABLE 8 microRNAs that are up-regulated in glioblastoma cells. Fold change microRNA Up 10X miR-10b, miR-10a, miR-96 Up 2-10X miR-182, miR-199b, miR-21, miR124, miR-199a, miR-199-s, miR-199a, miR-106b, miR-15b, miR-188, miR- 148a, miR-104, miR-224, miR-368, miR-23a, miR-210N, miR-183, miR- 25, miR-200cN, miR-373, miR-17-5p, let-7a, miR-16, miR-19b, miR-26a, miR-27a, miR-92, miR-93, miR-320 and miR-20 Up 1-2 X miR-143, miR-186. miR-337, miR- 30a-3p, miR-355, miR-324-3p etc.

TABLE 9 microRNAs that are down-regulated in glioblastoma cells. Fold change microRNA Down 10X miR-218, miR-124a, miR-124b, miR- 137, miR-184, miR-129, miR-33, miR- 139, miR-128b, miR-128a, miR-330, miR-133a, miR-203, miR-153, miR- 326, miR-105, miR-338, miR-133b, miR-132, miR-154, miR-29bN Down 2-10X miR-7N, miR-323, miR-219, miR-328, miR-149, miR-122a, miR-321, miR- 107, miR-190, miR-29cN, miR-95, miR-154, miR-221, miR-299, miR-31, miR-370, miR-331, miR-342, miR-340

TABLE 10 MMP genes contained within microvesicles isolated from glioblastoma cell line. Gene Symbol Accession ID Gene Description MMP1 AK097805 Homo sapiens cDNA FLJ40486 fis, clone TESTI2043866. [AK097805] MMP8 NM_002424 Homo sapiens matrix metallopeptidase 8 (neutrophil collagenase) (MMP8), mRNA [NM_002424] MMP12 NM_002426 Homo sapiens matrix metallopeptidase 12 (macrophage elastase) (MMP12), mRNA [NM_002426] MMP15 NM_002428 Homo sapiens matrix metallopeptidase 15 (membrane-inserted) (MMP15), mRNA [NM_002428] MMP20 NM_004771 Homo sapiens matrix metallopeptidase 20 (enamelysin) (MMP20), mRNA [NM_004771] MMP21 NM_147191 Homo sapiens matrix metallopeptidase 21 (MMP21), mRNA [NM_147191] MMP24 NM_006690 Homo sapiens matrix metallopeptidase 24 (membrane-inserted) (MMP24), mRNA [NM_006690] MMP26 NM_021801 Homo sapiens matrix metallopeptidase 26 (MMP26), mRNA [NM_021801] MMP27 NM_022122 Homo sapiens matrix metallopeptidase 27 (MMP27), mRNA [NM_022122] Note: Gene symbols are standard symbols assigned by Entrz Gene (http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene). Accession IDs are uniquely assigned to each gene by National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/sites/entrez?db=nuccore).

TABLE 11 Genes containing somatic mutations in glioblastoma adapted from the result of TCGA project (McLendon et al., 2008). Hugo Gene Symbol Entrez_Gene_Id A2M 2 A2M 2 A2M 2 ABCA3 21 ABCC4 10257 ABCC4 10257 ABCC4 10257 ADAM12 8038 ADAM15 8751 ADAMTSL3 57188 ADAMTSL3 57188 ADM 133 AIFM1 9131 AKAP2 11217 AKAP2 11217 ALK 238 ANK2 287 ANK2 287 ANK2 287 ANK2 287 ANK2 287 ANXA1 301 ANXA7 310 AOC3 8639 AOC3 8639 APBB1IP 54518 APC 324 ARNT 405 ASPM 259266 ASPM 259266 ASXL1 171023 ASXL1 171023 ATM 472 ATM 472 ATM 472 ATP6V1E1 529 ATR 545 AVIL 10677 AXL 558 BAI3 577 BAI3 577 BAI3 577 BAMBI 25805 BCAR1 9564 BCAR1 9564 BCL11A 53335 BCL11A 53335 BCL11A 53335 BCL11A 53335 BCL11A 53335 BCL11A 53335 BCL2L13 23786 BCR 613 BMPR1A 657 BRCA1 672 BRCA2 675 BRCA2 675 BRCA2 675 BTK 695 C18orf25 147339 C20orf160 140706 C20orf160 140706 C22orf24 25775 C6orf60 79632 C6orf60 79632 C9orf72 203228 CAND1 55832 CASP9 842 CAST 831 CAST 831 CAST 831 CBL 867 CBL 867 CCR5 1234 CD46 4179 CDC123 8872 CDKL5 6792 CDKN2A 1029 CDKN2A 1029 CDKN2A 1029 CENPF 1063 CENPF 1063 CENTG1 116986 CENTG1 116986 CES3 23491 CES3 23491 CHAT 1103 CHAT 1103 CHD5 26038 CHEK1 1111 CHEK1 1111 CHEK1 1111 CHEK1 1111 CHEK2 11200 CHEK2 11200 CHEK2 11200 CHEK2 11200 CHEK2 11200 CHEK2 11200 CHEK2 11200 CHEK2 11200 CHEK2 11200 CHEK2 11200 CHEK2 11200 CHEK2 11200 CHEK2 11200 CHEK2 11200 CHEK2 11200 CHEK2 11200 CHI3L2 1117 CHIC2 26511 CHL1 10752 CHL1 10752 CMTM3 123920 CNTFR 1271 COL11A1 1301 COL1A1 1277 COL1A1 1277 COL1A1 1277 COL1A1 1277 COL1A2 1278 COL1A2 1278 COL3A1 1281 COL3A1 1281 COL3A1 1281 COL3A1 1281 COL5A1 1289 COL6A2 1292 COL6A2 1292 COL6A2 1292 CRLF1 9244 CSF3R 1441 CSF3R 1441 CSMD3 114788 CSMD3 114788 CSNK1E 1454 CTNNB1 1499 CTSH 1512 CTSH 1512 CYLD 1540 CYP27B1 1594 CYP27B1 1594 CYP3A4 1576 DCX 1641 DDIT3 1649 DDR2 4921 DDR2 4921 DDR2 4921 DES 1674 DES 1674 DGKD 8527 DGKG 1608 DHTKD1 55526 DMBT1 1755 DMRT3 58524 DOCK1 1793 DOCK1 1793 DOCK1 1793 DOCK8 81704 DOCK8 81704 DPYSL4 10570 DPYSL4 10570 DST 667 DST 667 DST 667 DST 667 DST 667 DST 667 DST 667 DST 667 DTX3 196403 EGFR 1956 EGFR 1956 EGFR 1956 EGFR 1956 EGFR 1956 EGFR 1956 EGFR 1956 EGFR 1956 EGFR 1956 EGFR 1956 EGFR 1956 EGFR 1956 EGFR 1956 EGFR 1956 EGFR 1956 EGFR 1956 EGFR 1956 EGFR 1956 EGFR 1956 EGFR 1956 EGFR 1956 EGFR 1956 EGFR 1956 ELAVL2 1993 EP300 2033 EP300 2033 EP400 57634 EP400 57634 EP400 56734 EPHA2 1969 EPHA3 2042 EPHA3 2042 EPHA4 2043 EPHA4 2043 EPHA6 285220 EPHA7 2045 EPHA7 2045 EPHA8 2046 EPHA8 2046 EPHB1 2047 ERBB2 2064 ERBB2 2064 ERBB2 2064 ERBB2 2064 ERBB2 2064 ERBB2 2064 ERBB2 2064 ERBB2 2064 ERBB2 2064 ERBB2 2064 ERBB2 2064 ERBB3 2065 ESR1 2099 ETNK2 55224 EYA1 2138 EYA1 2138 F13A1 2162 FBXW7 55294 FBXW7 55294 FGFR1 2260 FGFR1 2260 FGFR2 2263 FGFR3 2261 FKBP9 11328 FKBP9 11328 FKBP9 11328 FKBP9 11328 FKBP9 11328 FKBP9 11328 FKBP9 11328 FKBP9 11328 FKBP9 11328 FKBP9 11328 FKBP9 11328 FKBP9 11328 FKBP9 11328 FLI1 2313 FLI1 2313 FLT1 2321 FLT4 2324 FN1 2335 FN1 2335 FN1 2335 FN1 2335 FN1 2335 FN1 2335 FOXO3 2309 FOXO3 2309 FOXO3 2309 FRAP1 2475 FURIN 5045 FURIN 5045 FURIN 5045 GARNL3 84253 GATA3 2625 GATA3 2625 GCLC 2729 GDF10 2662 GLI1 2735 GLI3 2737 GLTSCR2 29997 GNAI1 2770 GNAS 2778 GNAS 2778 GPR78 27201 GRIA2 2891 GRLF1 2909 GRN 2896 GRN 2896 GSTM5 2949 GSTM5 2949 GSTM5 2949 GSTM5 2949 GSTM5 2949 GSTM5 2949 GSTM5 2949 GSTM5 2949 GSTM5 2949 GYPC 2995 HCK 3055 HCK 3055 HELB 92797 HLA-E 3133 HLA-E 3133 HLA-E 3133 HLA-E 3133 HS3ST3A1 9955 HSP90AA1 3320 HSP90AA1 3320 HSPA8 3312 HSPA8 3312 HSPA8 3312 HSPA8 3312 HSPA8 3312 HSPA8 3312 HSPA8 3312 ID3 3399 IFITM3 10410 IFITM3 10410 IFITM3 10410 IFITM3 10410 IFITM3 10410 IFITM3 10410 IFITM3 10410 IL1RL1 9173 IL31 386653 ILK 3611 ING4 51147 ING4 51147 ING4 51147 INHBE 83729 IQGAP1 8826 IRAK3 11213 IRS1 3667 IRS1 3667 ISL1 3670 ITGAL 3683 ITGB2 3689 ITGB2 3689 ITGB2 3689 ITGB3 3690 ITGB3 3690 ITGB3 3690 ITGB3 3690 ITGB3 3690 JAG1 182 KIAA1632 57724 KIF3B 9371 KIT 3815 KIT 3815 KIT 3815 KLF4 9314 KLF4 9314 KLF6 1316 KLF6 1316 KLK8 11202 KPNA2 3838 KPNA2 3838 KRAS 3845 KSR2 283455 KSR2 283455 KTN1 3895 LAMP1 3916 LAMP1 3916 LAX1 54900 LCK 3932 LDHA 3939 LDHA 3939 LGALS3BP 3959 LGALS3BP 3959 LGALS3BP 3959 LRRN2 10446 LTF 4057 LTF 4057 LYN 4067 MAG 4099 MAP3K6 9064 MAPK13 5603 MAPK7 5598 MAPK8IP2 23542 MAPK8IP3 23162 MAPK9 5601 MAPK9 5601 MARK1 4139 MARK1 4139 MDM2 4193 MDM4 4194 MEOX2 4223 MET 4233 MET 4233 MET 4233 MLH1 4292 MLH1 4292 MLH1 4292 MLL4 9757 MLL4 9757 MLL4 9757 MLLT7 4303 MMD2 221938 MN1 4330 MSH2 4436 MSH2 4436 MSH6 2956 MSH6 2956 MSH6 2956 MSH6 2956 MSI1 4440 MSI1 4440 MTAP 4507 MUSK 4593 MYCN 4613 MYCN 4613 MYLK2 85366 MYO3A 53904 MYST4 23522 MYST4 23522 MYST4 23522 MYST4 23522 NBN 4683 NDUFA10 4705 NEK10 152110 NELL2 4753 NF1 4763 NF1 4763 NF1 4763 NF1 4763 NF1 4763 NF1 4763 NF1 4763 NF1 4763 NF1 4763 NF1 4763 NF1 4763 NF1 4763 NF1 4763 NF1 4763 NF1 4763 NF1 4763 NMBR 4829 NMBR 4829 NOS3 4846 NOS3 4846 NOTCH1 4851 NOTCH1 4851 NRXN3 9369 NTRK3 4916 NUMA1 4926 NUP214 8021 ONECUT2 9480 OR5P2 120065 PAX5 5079 PDGFRA 5156 PDGFRA 5156 PDGFRA 5156 PDGFRB 5159 PDGFRB 5159 PDK2 5164 PDPK1 5170 PDZD2 23037 PDZD2 23037 PHLPP 23239 PI15 51050 PI15 51050 PIK3C2A 5286 PIK3C2B 5287 PIK3C2G 5288 PIK3C2G 5288 PIK3C2G 5288 PIK3C2G 5288 PIK3C2G 5288 PIK3CA 5290 PIK3CA 5290 PIK3CA 5290 PIK3CA 5290 PIK3CA 5290 PIK3R1 5295 PIK3R1 5295 PIK3R1 5295 PIK3R1 5295 PIK3R1 5295 PIK3R1 5295 PIM1 5292 PLAG1 5324 PML 5371 PMS2 5395 POU2F1 5451 PPP2R5D 5528 PRKCA 5578 PRKCA 5578 PRKCB1 5579 PRKCB1 5579 PRKCD 5580 PRKCD 5580 PRKCD 5580 PRKCD 5580 PRKCD 5580 PRKCD 5580 PRKCZ 5590 PRKCZ 5590 PRKD2 25865 PRKD2 25865 PRKDC 5591 PRKDC 5591 PRKDC 5591 PROX1 5629 PSMD13 5719 PSMD13 5719 PSMD13 5719 PTCH1 5727 PTCH1 5727 PTEN 5728 PTEN 5728 PTEN 5728 PTEN 5728 PTEN 5728 PTEN 5728 PTEN 5728 PTEN 5728 PTEN 5728 PTEN 5728 PTEN 5728 PTEN 5728 PTEN 5728 PTEN 5728 PTEN 5728 PTEN 5728 PTEN 5728 PTEN 5728 PTEN 5728 PTEN 5728 PTEN 5728 PTEN 5728 PTEN 5728 PTEN 5728 PTEN 5728 PTEN 5728 PTEN 5728 PTEN 5728 PTEN 5728 PTEN 5728 PTEN 5728 PTEN 5728 PTEN 5728 PTK2B 2185 PTPN11 5781 PTPN11 5781 RADIL 55698 RADIL 55698 RB1 5925 RB1 5925 RB1 5925 RB1 5925 RB1 5925 RB1 5925 RB1 5925 RB1 5925 RB1 5925 RINT1 60561 RIPK4 54101 RNF38 152006 ROR2 4920 ROR2 4920 ROS1 6098 ROS1 6098 RPN1 6184 RPS6KA3 6197 RTN1 6252 RUNX1T1 862 RYR3 6263 RYR3 6263 SAC 55811 SAC 55811 SEMA3B 7869 SERPINA3 12 SERPINE1 5054 SHH 6469 SLC12A6 9990 SLC12A6 9990 SLC25A13 10165 SLC25A13 10165 SLC2A2 6514 SLIT2 9353 SLIT2 9353 SLIT2 9353 SMAD2 4087 SMAD4 4089 SNF1LK2 23235 SNF1LK2 23235 SNX13 23161 SOCS1 8651 SOX11 6664 SOX11 6664 SPARC 6678 SPDEF 25803 SPN 6693 SPRED3 399473 SRPK2 6733 ST7 7982 STAT1 6772 STAT3 6774 STK32B 55351 STK36 27148 SYP 6855 TAF1 6872 TAF1 6872 TAOK3 51347 TAS1R1 80835 TBK1 29110 TBK1 29110 TCF12 6938 TCF12 6938 TCF12 6938 TERT 7015 TERT 7015 TGFBR2 7048 TIMP2 7077 TNC 3371 TNC 3371 TNC 3371 TNFRSF11B 4982 TNK2 10188 TNK2 10188 TNK2 10188 TNK2 10188 TOP1 7150 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TPBG 7162 TRIM24 8805 TRIM3 10612 TRIM33 51592 TRIP6 7205 TRRAP 8295 TRRAP 8295 TSC1 7248 TSC2 7249 TSC2 7249 TSC2 7249 UNG 7374 UPF2 26019 UPF2 26019 VAV2 7410 VLDLR 7436 WNT2 7472 ZEB1 6935 ZEB1 6935 ZNF384 171017 ZNF384 171017 Note: Hugo Gene Symbols are assigned to individual genes by HUGO Gene Nomenclature Committee (http://www.genenames.org/). Entrez_Gene_Ids are assigned to individual genes by Entrz Gene (http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene).

TABLE 12 Genes containing somatic mutations in glioblastoma adapted from the paper by Parsons et. al. (Parsons et al., 2008) Gene symbol Accession ID A2M NM_000014 A4GALT CCDS14041.1 A4GNT CCDS3097.1 AACS CCDS9263.1 ABCA10 CCDS11684.1 ABCA12 NM_015657 ABCA13 NM_152701 ABCA4 CCDS747.1 ABCA5 CCDS11685.1 ABCA7 CCDS12055.1 ABCA9 CCDS11681.1 ABCB1 CCDS5608.1 ABCB6 CCDS2436.1 ABCC10 CCDS4896.1 ABCC11 CCDS10732.1 ABCC3 NM_003786 ABCC5 NM_005688 ABCD2 CCDS8734.1 ABCF2 CCDS5922.1 ABCG2 CCDS3628.1 ABHD3 NM_138340 ABHD4 CCDS9572.1 ABHD7 CCDS736.1 ABL2 NM_007314 ABTB2 CCDS7890.1 ACAD9 CCDS3053.1 ACADS CCDS9207.1 ACADSB CCDS7634.1 ACAT2 CCDS5268.1 ACCN1 CCDS11276.1 ACCN3 CCDS5914.1 ACF CCDS7241.1 ACLY CCDS11412.1 ACOX3 CCDS3401.1 ACP5 CCDS12265.1 ACRBP CCDS8554.1 ACTG1 CCDS11782.1 ACTN1 CCDS9792.1 ACTR10 NM_018477 ACTR1A CCDS7536.1 ACTR8 CCDS2875.1 ACTRT1 CCDS14611.1 ADAM12 CCDS7653.1 ADAM15 CCDS1084.1 ADAM18 CCDS6113.1 ADAM28 NM_014265 ADAM29 CCDS3823.1 ADAMTS1 NM_006988 ADAMTS13 CCDS6970.1 ADAMTS17 CCDS10383.1 ADAMTS20 NM_175851 ADAMTS4 CCDS1223.1 ADAMTS8 NM_007037 ADAR CCDS1071.1 ADARB2 CCDS7058.1 ADCY1 NM_021116 ADCY8 CCDS6363.1 ADRBK2 CCDS13832.1 AGC1 NM_001135 AGL CCDS759.1 AGPAT1 CCDS4744.1 AGPS CCDS2275.1 AGRN NM_198576 AHDC1 NM_001029882 AHI1 NM_017651 AIM1L NM_017977 AKAP11 CCDS9383.1 AKAP13 NM_007200 AKAP4 CCDS14329.1 AKAP9 CCDS5622.1 AKNA CCOS6805.1 AKR7A2 CCDS194.1 ALDH18A1 CCDS7443.1 ALDH1A2 CCDS10163.1 ALDH1L1 CCDS3034.1 ALDH2 CCDS9155.1 ALLC NM_018436 ALOX12 CCDS11084.1 ALOXE3 CCDS11130.1 ALPI CCDS2492.1 ALPK2 CCDS11966.1 ALPK3 CCDS10333.1 ALPL CCDS217.1 ALS2CL CCDS2743.1 ALS2CR12 CCDS2346.1 AMACO CCDS7589.1 AMID CCDS7297.1 ANK2 CCOS3702.1 ANK3 CCDS7258.1 ANKMY1 CCDS2536.1 ANKRD10 CCDS9520.1 ANKRD11 NM_013275 ANKRD12 CCDS11843.1 ANKRD15 CCDS6441.1 ANKRD28 NM_015199 ANP32D NM_012404 AP3B1 CCDS4041.1 APG7L CCDS2605.1 API5 NM_006595 APOB CCDS1703.1 APOBEC3G CCDS13984.1 APRG1 NM_178339 AQP10 CCDS1065.1 AR CCDS14387.1 ARD1B ENST00000286794 ARHGAP4 CCDS14736.1 ARHGAP5 NM_001173 ARHGAP8 CCDS14058.1 ARHGDIG CCDS10404.1 ARHGEF9 NM_015185 ARID1A CCDS285.1 ARL1 NM_001177 ARNT2 NM_014862 ARP10 CCDS13985.1 ARSE CCDS14122.1 ASB4 CCDS5641.1 ASCL4 NM_203436 ASCL5 ENST00000344317 ASGR1 CCDS11089.1 ASH1L CCDS1113.1 ASIP CCDS13232.1 ASTN CCDS1319.1 ATAD2B ENST00000295142 ATP10B ENST00000327245 ATP12A NM_001676 ATP13A1 NM_020410 ATP13A2 CCDS175.1 ATP1A2 CCDS1196.1 ATP2A1 CCDS10643.1 ATP2A3 CCDS11041.1 ATP2B1 CCDS9035.1 ATP2B2 CCDS2601.1 ATP6V1G3 CCDS1396.1 ATP7B NM_000053 ATP8A1 CCDS3466.1 ATP8B1 CCDS11965.1 ATRNL1 CCDS7592.1 ATXN1 NM_000332 AUTS2 CCDS5539.1 AXIN2 CCDS11662.1 AZI1 NM_001009811 B3Gn-T6 NM_138706 BAD CCDS8065.1 BAI2 CCDS346.1 BAMBI CCDS7162.1 BAT2D1 CCDS1296.1 BAZ1A CCDS9651.1 BCAR3 CCDS745.1 BCL2L1 CCDS13188.1 BCL2L12 CCDS12776.1 BCL2L2 CCDS9591.1 BCL6 CCDS3289.1 BCOR CCDS14250.1 BFSP1 CCDS13126.1 BIN1 CCDS2137.1 BIRC1 CCDS4009.1 BIRC6 NM_016252 BMP3 CCDS3588.1 BMPER CCDS5442.1 BNC2 CCDS6482.1 BOC CCDS2971.1 BPY2IP1 NM_018174 BRAF CCDS5863.1 BRF1 CCDS10001.1 BRP44L CCDS5293.1 BRPF1 CCDS2575.1 BSN CCDS2800.1 BST1 CCDS3416.1 BTAF1 CCDS7419.1 BTBD1 CCDS10322.1 BTBD3 CCDS13113.1 BTC CCDS3566.1 BTK CCDS14482.1 BTNL2 CCDS4749.1 BTNL9 CCDS4460.1 BUCS1 CCDS10587.1 C10orf18 ENST00000263123 C10orf26 CCDS7540.1 C10orf33 CCDS7474.1 C10orf47 CCDS7085.1 C10orf64 ENST00000265453 C10orf71 ENST00000323868 C10orf80 NM_001008723 C10orf81 CCDS7583.1 C11orf11 NM_006133 C11ORF4 CCDS8066.1 C12orf11 CCDS8708.1 C12orf42 NM_198521 C14orf115 CCDS9830.1 C14orf131 NM_018335 C14orf133 CCDS9862.1 C14orf145 NM_152446 C14orf155 CCDS9679.1 C14orf159 NM_024952 C14oef31 CCDS9704.1 C14orf43 CCDS9819.1 C14orf49 CCDS9935.1 C15orf2 CCDS10015.1 C15orf42 ENST00000268138 C16orf9 CCDS10402.1 C17orf27 NM_020914 C17orf31 CCDS11016.1 C18orf25 NM_001008239 C18orf4 CCDS11995.1 C19orf29 ENST00000221899 C1orf147 NM_001025592 C1orf151 NM_001032363 C1orf16 CCDS1355.1 C1orf173 NM_001002912 C1orf84 NM_015284 C1QDC1 CCDS8720.1 C20orf10 CCDS13352.1 C20orf102 CCDS13299.1 C20orf114 CCDS13218.1 C20orf23 CCDS13122.1 C20orf78 ENST00000278779 C21orf29 CCDS13712.1 C21orf5 CCDS13643.1 C21orf69 NM_058189 C2orf17 CCDS2434.1 C2orf2 CCDS2050.1 C2orf3 CCDS1961.1 C3orf14 CCDS2896.1 C4orf7 CCDS3537.1 C5AR1 NM_001736 C6 CCDS3936.1 C6orf103 ENST00000326929 C6orf150 CCDS4978.1 C6orf163 NM_001010868 C6orf165 CCDS5009.1 C6orf168 NM_032511 C6orf170 NM_152730 C6orf21 NM_001003693 C6orf213 NM_001010852 C6orf29 CCDS4724.1 C6orf4 CCDS5092.1 C6orf68 CCDS5118.1 C7orf16 CCDS5436.1 C8A CCDS606.1 C8B NM_000066 C8orf77 NM_001039382 C8ORFK23 NM_001039112 C9orf126 NM_173690 C9orf19 CCDS6598.1 C9orf5 NM_032012 C9orf50 NM_199350 CA2 CCDS6239.1 CAB39 CCDS2478.1 CABIN1 CCDS13823.1 CABP1 CCDS9204.1 CACNA1A NM_000068 CACNA1C NM_000719 CACNA1E NM_000721 CACNA1H NM_021098 CACNA1I NM_001003406 CACNA1S CCDS1407.1 CACNA2D3 NM_018398 CACNB2 CCDS7125.1 CACNG4 CCDS11667.1 CADPS CCDS2898.1 CADPS2 NM_017954 CALM1 CCDS9892.1 CAMSAP1 NM_015447 CAPN12 CCDS12519.1 CAPN3 CCDS10084.1 CAPN3 CCDS10084.1 CAPZA3 CCDS8681.1 CARD11 CCDS5336.1 CART1 CCDS9028.1 CASC5 NM_170589 CASQ1 CCDS1198.1 CCDC15 NM_025004 CCNF CCDS10467.1 CCNL2 ENST00000321423 CCNYL1 ENST00000339882 CD19 CCDS10644.1 CD84 CCDS1206.1 CD96 CCDS2958.1 CDA08 CCDS10728.1 CDC2L6 CCDS5085.1 CDC7 CCDS734.1 CDCA8 CCDS424.1 CDH23 NM_022124 CDH24 CCDS9585.1 CDH26 CCDS13485.1 CDH5 CCDS10804.1 CDK5 NM_004935 CDK6 CCDS5628.1 CDT1 NM_030928 CDX1 CCDS4304.1 CDYL2 NM_152342 CEACAM1 CCDS12609.1 CELSR3 CCDS2775.1 CENPF NM_016343 CENTG3 NM_031946 CEP135 NM_025009 Cep164 NM_014956 CEP2 CCDS13255.1 CETP CCDS10772.1 CFTR CCDS5773.1 CGI-38 CCDS10835.1 CGI-96 CCDS14036.1 CGNL1 CCDS10161.1 CHAD CCDS11568.1 CHD4 CCDS8552.1 CHD5 CCDS57.1 CHD6 CCDS13317.1 CHD9 NM_025134 CHDH CCDS2873.1 CHEK1 CCDS8459.1 ChGn CCDS6010.1 CHKA CCDS8178.1 CHL1 CCDS2556.1 CHRM2 CCDS5843.1 CHRM5 CCDS10031.1 CHRNA3 CCDS10305.1 CHRNA4 CCDS13517.1 CHRNA9 CCDS3459.1 CHST13 CCDS3039.1 CIDEA CCDS11856.1 CIDEC CCDS2587.1 CIZ1 CCDS6894.1 CKLFSF5 CCDS9599.1 CLASP1 NM_015282 CLASP2 NM_015097 CLCN1 CCDS5881.1 CLCN5 CCDS14328.1 CLDN11 CCDS3213.1 CLEC1A CCDS8612.1 CLEC4E CCDS8594.1 CLEC7A CCDS8613.1 CLIC6 CCDS13638.1 CLN8 CCDS5956.1 CLSPN CCDS396.1 CLSTN2 CCDS3112.1 CLTA CCDS6600.1 CMIP NM_198390 CMYA1 CCDS2683.1 CMYA4 CCDS11292.1 CNNM2 CCDS7543.1 CNOT1 CCDS10799.1 CNOT10 CCDS2655.1 CNOT7 CCDS6000.1 CNR2 CCDS245.1 CNTN4 CCDS2558.1 CNTNAP2 CCDS5889.1 COCH CCDS9640.1 COG5 CCDS5742.1 COG5 CCDS5742.1 COH1 CCDS6280.1 COL14A1 NM_021110 COL18A1 NM_030582 COL23A1 CCDS4436.1 COL24A1 NM_152890 COL3A1 CCDS2297.1 COL4A2 NM_001846 COL4A4 NM_000092 COL4A5 CCDS14543.1 COL5A3 CCDS12222.1 COL6A3 NM_004369 COL6A3 NM_057167 COL8A2 CCDS403.1 COPB CCDS7815.1 COQ2 NM_015697 CPB1 NM_001871 CPN1 CCDS7486.1 CPNE2 CCDS10774.1 CPNE4 CCDS3072.1 CPS1 CCDS2393.1 CPSF4 CCDS5664.1 CPT1B CCDS14098.1 CPT1C CCDS12779.1 CRA CCDS942.1 CRAT CCDS6919.1 CREB1 CCDS2374.1 CRIM2 ENST00000257704 CRISPLD1 CCDS6219.1 CRR9 CCDS3862.1 CRX CCDS12706.1 CRY2 CCDS7915.1 CRYAA CCDS13695.1 CSK CCDS10269.1 CSMD1 NM_033225 CSN3 CCDS3538.1 CSNK2A2 CCDS10794.1 CSPG2 CCDS4060.1 CSPG5 CCDS2757.1 CSPG6 NM_005445 CSTF1 CCDS13452.1 CTEN CCDS11368.1 CTNNA2 NM_004389 CTNNA3 CCDS7269.1 CTSW CCDS8117.1 CUBN CCDS7113.1 CUGBP1 CCDS7938.1 CUGBP1 CCDS7939.1 CUL4B NM_003588 CUTL1 CCDS5721.1 CX40.1 CCDS7191.1 CXCR3 CCDS14416.1 CXorfl7 CCDS14356.1 CXorf20 CCDS14184.1 CXorf27 ENST00000341016 CXorf37 CCDS14322.1 CXXC5 NM_016463 CYBB CCDS14242.1 CYP26C1 CCDS7425.1 CYP2C19 CCDS7436.1 CYP2R1 CCDS7818.1 CYP4F12 NM_023944 DAB2IP CCDS6832.1 DCBLD2 NM_080927 DCC CCDS11952.1 DCT CCDS9470.1 DCTN4 CCDS4310.1 DDB1 NM_001923 DDR1 CCDS4690.1 DDX1 CCDS1686.1 DDX31 CCDS6951.1 DDX54 NM_024072 DEFB112 NM_001037498 DEFB125 CCDS12989.1 DELGEF CCDS7828.1 DEPDC5 NM_014662 DFNB31 CCDS6806.1 DGCR6 CCDS13753.1 DGKD CCDS2504.1 DHPS CCDS12276.1 DHX29 NM_019030 DIO3 NM_001362 DKFZp434I099 CCDS10787.1 DKFZp547A023 CCDS845.1 DKFZp547B1713 CCDS1591.1 DKFZP564B1023 CCDS1403.1 DKFZp564I1922 CCDS14124.1 DKFZp761L1417 CCDS5658.1 DKFZp761N1114 CCDS1455.1 DLD CCDS5749.1 DLEC1 ENST00000337335 DLGAP2 NM_004745 DMN NM_015286 DMTF1 CCDS5601.1 DNAH1 NM_015512 DNAH10 CCDS9255.1 DNAH11 NM_003777 DNAH3 CCDS10594.1 DNAH5 CCDS3882.1 DNAH8 CCDS4838.1 DNAH9 CCDS11160.1 DNAI2 CCDS11697.1 DNCH1 CCDS9966.1 DNCLI2 CCDS10818.1 DNHD3 NM_020877 DNTTIP1 CCDS13369.1 DOCK4 NM_014705 DOCK8 CCDS6440.1 DOCK9 NM_015296 DOK6 NM_152721 DONSON CCDS13632.1 DRCTNNB1A CCDS5377.1 DRD3 CCDS2978.1 DRG1 CCDS13897.1 DSG1 CCDS11896.1 DSG2 NM_001943 DSG3 CCDS11898.1 DSG4 CCDS11897.1 DSPP NM_014208 DST CCDS4959.1 DTX1 CCDS9164.1 DTX4 ENST00000227451 DULLARD CCDS11093.1 DUSP22 CCDS4468.1 DUSP3 CCDS11469.1 DYRK3 NM_001004023 DZIP3 CCDS2952.1 E2F4 NM_001950 EAF1 CCDS2626.1 EBF CCDS4343.1 EBF3 NM_001005463 ECEL1 CCDS2493.1 ECHDC2 CCDS571.1 ECOP NM_030796 EDD1 NM_015902 EDG3 CCDS6680.1 EDG8 CCDS12240.1 EEF1A1 ENST00000331523 EFCBP1 NM_022351 EFHC2 NM_025184 EGF CCDS3689.1 EGFR CCDS5514.1 EHBP1L1 ENST00000309295 EIF2A NM_032025 EIF3S12 CCDS12517.1 EIF4G1 CCDS3259.1 EIF4G2 NM_001418 EME2 NM_001010865 EML4 CCDS1807.1 EMR4 ENST00000359590 EN2 CCDS5940.1 ENO1 CCDS97.1 ENPP2 CCDS6329.1 ENPP6 CCDS3834.1 ENPP7 CCDS11763.1 ENSA CCDS958.1 ENST00000294635 ENST00000294635 ENST00000310882 ENST00000310882 ENST00000326382 ENST00000326382 ENST00000328067 ENST00000328067 ENST00000331583 ENST00000331583 ENST00000334627 ENST00000334627 ENST00000336168 ENST00000336168 ENST00000355177 ENST00000355177 ENST00000355324 ENST00000355324 ENST00000355607 ENST00000355607 ENST00000357689 ENST00000357689 ENST00000358347 ENST00000358347 ENST00000359736 ENST00000359736 EPB41L2 CCDS5141.1 EPB41L4B NM_019114 EPB49 CCDS6020.1 EPC1 CCDS7172.1 EPHA2 CCDS169.1 EPHA5 CCDS3513.1 EPHA6 ENST00000334709 EPHA8 CCDS225.1 EPO CCDS5705.1 ERCC5 NM_000123 ERF CCDS12600.1 ERN1 NM_001433 ESCO2 NM_001017420 ESPNP ENST00000270691 ESR1 CCDS5234.1 ESR2 CCDS9762.1 ETV1 NM_004956 EVI1 CCDS3205.1 EVPL CCDS11737.1 EXOC6B ENST00000272427 EXTL1 CCDS271.1 F13B CCDS1388.1 F2RL1 CCDS4033.1 F3 CCDS750.1 F5 CCDS1281.1 FAD158 CCDS725.1 FADS1 CCDS8011.1 FAM43A NM_153690 FAM46B CCDS294.1 FAM47A NM_203408 FAM48A ENST00000360252 FAM63B NM_019092 FAM78B NM_001017961 FAM92B NM_198491 FANCA NM_000135 FANCD2 CCDS2595.1 FASN CCDS11801.1 FAT NM_005245 FBN3 CCDS12196.1 FBXO40 NM_016298 FBXW7 CCDS3777.1 FCGBP CCDS12546.1 FCHSD1 NM_033449 FECH CCDS11964.1 FEZ1 NM_005103 FGD1 CCDS14359.1 FGD4 CCDS8727.1 FGF2 NM_002006 FGFR3 CCDS3353.1 FGIF CCDS8300.1 FIGF CCDS14166.1 FLII CCDS11192.1 FLJ10276 CCDS363.1 FLJ10514 CCDS1311.1 FLJ11088 CCDS8716.1 FIJ11535 CCDS12043.1 FLJ12529 CCDS8006.1 FLJ12644 CCDS12843.1 FLJ12671 CCDS1153.1 FLJ12700 CCDS5898.1 FLJ13273 CCDS3672.1 FLJ13576 CCDS5757.1 FLJ13725 CCDS10840.1 FLJ13841 CCDS11819.1 FLJ13941 CCDS40.1 FLJ14397 CCDS1945.1 FLJ16165 NM_001004318 FLJ16331 NM_001004326 FLJ16478 NM_001004341 FLJ20035 NM_017631 FLJ20097 ENST00000317751 FLJ20186 CCDS10989.1 FLJ20232 CCDS13995.1 FLJ20272 NM_017735 FLJ20294 NM_017749 FLJ20298 CCDS14522.1 FLJ21159 CCDS3792.1 FLJ21963 CCDS9022.1 FLJ22709 CCDS12351.1 FLJ23049 CCDS3199.1 FLJ23447 CCDS12300.1 FLJ23577 ENST00000303168 FLJ23577 CCDS3910.1 FLJ23790 CCDS6346.1 FLJ25715 NM_182570 FLJ25801 CCDS3850.1 FLJ27465 NM_001039843 FLJ30525 CCDS787.1 FLJ30655 CCDS3740.1 FLJ30707 CCDS9427.1 FLJ31438 NM_152385 FLJ32796 CCDS1507.1 FLJ32934 CCDS1082.1 FLJ33167 CCDS3837.1 FLJ33387 CCDS9783.1 FLJ34512 CCDS10424.1 FLJ34658 CCDS3913.1 FLJ35709 CCDS7767.1 FLJ35728 CCDS1537.1 FLJ36004 CCDS8704.1 FLJ36208 NM_145270 FLJ36601 CCDS14238.1 FLJ37440 CCDS2095.1 FLJ38964 NM_173527 FLJ38973 NM_153689 FLJ39058 CCDS8489.1 FLJ39198 NM_001039769 FLJ39873 CCDS2980.1 FLJ40243 NM_173489 FLJ40342 CCDS11512.1 FLJ40869 CCDS1691.1 FLJ41170 NM_001004332 FLJ41766 ENST00000338573 FLJ43706 NM_001039774 FLJ44186 CCDS5854.1 FLJ44861 CCDS11778.1 FLJ45300 NM_001001681 FLJ45744 CCDS12424.1 FLJ45964 CCDS2530.1 FLJ45974 NM_001001707 FLJ46072 CCDS6410.1 FLJ90650 CCDS4124.1 FLT1 CCDS9330.1 FMN2 NM_020066 FMNL2 NM_001004417 FN1 CCDS2399.1 FNBP1 NM_015033 FNDC1 NM_032532 FOXA2 CCDS13147.1 FOXB1 NM_012182 FOXI1 CCDS4372.1 FOXM1 CCDS8515.1 FOXR2 NM_198451 FRAS1 NM_025074 FREM2 NM_207361 FRMD3 NM_174938 FRMD4B ENST00000264546 FRMPD1 CCDS6612.1 FRMPD4 NM_014728 FSD2 NM_001007122 FSTL1 CCDS2998.1 FSTL4 NM_015082 FSTL5 CCDS3802.1 FUBP1 CCDS683.1 FUT2 NM_000511 FXYD6 CCDS8387.1 FYCO1 CCDS2734.1 FZD10 CCDS9267.1 FZD3 CCDS6069.1 FZD6 CCDS6298.1 FZD9 CCDS5548.1 G3BP2 CCDS3571.1 GABPA CCDS13575.1 GABRA6 CCDS4356.1 GABRD CCDS36.1 GAD2 CCDS7149.1 GALNT13 CCDS2199.1 GALNT3 CCDS2226.1 GALNT7 CCDS3815.1 GALNTL1 NM_020692 GANAB CCDS8026.1 GAPVD1 NM_1115635 GAS6 CCDS9540.1 GATA4 CCDS5983.1 GATA6 CCDS11872.1 GBF1 CCDS7533.1 GCGR NM_000160 GCM1 CCDS4950.1 GCM2 CCDS4517.1 GCNT3 CCDS10172.1 GDF3 CCDS8581.1 GEFT CCDS8947.1 GFI1B CCDS6957.1 GFM1 NM_024996 GGA2 CCDS10611.1 GGPS1 CCDS1604.1 GHSR CCDS3218.1 GIMAP1 CCDS5906.1 GIMAP5 CCDS5907.1 GIMAP8 NM_175571 GIT2 CCDS9138.1 GJA4 NM_002060 GJB4 CCDS383.1 GK CCDS14225.1 GLRA1 CCDS4320.1 GMCL1L CCDS4433.1 GMDS CCDS4474.1 GML CCDS6391.1 GNAI2 CCDS2813.1 GNAT1 CCDS2812.1 GNL2 CCDS421.1 GNPTG CCDS10436.1 GNS CCDS8970.1 GOLGA3 CCDS9281.1 GOLGA4 CCDS2666.1 GORASP2 NM_015530 GOT2 CCDS10801.1 GP6 NM_016363 GPBP1 NM_022913 GPI7 CCDS3336.1 GPR114 CCDS10785.1 GPR116 CCDS4919.1 GPR132 CCDS9997.1 GPR142 CCDS11698.1 GPR144 NM_182611 GPR145 CCDS5044.1 GPR174 CCDS14443.1 GPR37 CCDS5792.1 GPR37L1 CCDS1420.1 GPR40 CCDS12458.1 GPR43 CCDS12461.1 GPR61 CCDS801.1 GPR73L1 CCDS13089.1 GPR74 CCDS3551.1 GPR78 CCDS3403.1 GPR83 CCDS8297.1 GPR85 CCDS5758.1 GPRC5C CCDS11699.1 GPS1 CCDS11800.1 GPS2 NM_032442 GPSM2 CCDS792.1 GPT CCDS6430.1 GRAP2 CCDS13999.1 GRASP CCDS8817.1 GRCA CCDS8563.1 GREB1 NM_014668 GRIA4 CCDS8333.1 GRIK4 CCDS8433.1 GRIN2B CCDS8662.1 GRIN3A CCDS6758.1 GRINA NM_001009184 GRM1 CCDS5209.1 GRM3 CCDS5600.1 GSR NM_000637 GSTO2 CCDS7556.1 GTF2A2 CCDS10173.1 GTF2H4 NM_020442 GTF3C4 CCDS6953.1 GUCY1A3 NM_000856 GUCY1B2 CCDS9426.1 GZMH CCDS9632.1 HAMP CCDS12454.1 HBB NM_000519 HBXAP CCDS8253.1 HCFC2 CCDS9097.1 HDAC2 NM_001527 HDAC9 NM_178425 HDC CCDS10134.1 HECW2 NM_020760 HERC1 NM_003922 HERC2 CCDS10021.1 HGSNAT ENST00000332689 HHIP CCDS3762.1 HIF3A CCDS12681.1 HIP1 NM_005338 HIVEP1 NM_002114 HIVEP2 NM_006734 HIVEP3 CCDS463.1 HMG20A CCDS10295.1 HMGCL CCDS243.1 HMP19 CCDS4391.1 HNT CCDS8491.1 HORMAD1 CCDS967.1 HOXA6 CCDS5407.1 HP NM_005143 HP1BP3 NM_016287 HPCAL4 CCDS441.1 HRB CCDS2467.1 HRBL CCDS5697.1 HRG CCDS3280.1 HS2ST1 CCDS712.1 HS2ST1 CCDS711.1 HSA9761 CCDS3981.1 HSD17B2 CCDS10936.1 HSD17B8 CCDS4769.1 HSPA4L CCDS3734.1 HSPC111 NM_016391 HSPG2 NM_005529 HTR3C CCDS3250.1 HTR3E CCDS3251.1 HXMA CCDS10586.1 HYPB CCDS2749.1 IBTK NM_015525 ICAM3 CCDS12235.1 ICEBERG NM_021571 IDE CCDS7421.1 IDH1 CCDS2381.1 IFI44 CCDS688.1 IFIT3 CCDS7402.1 IFNAR1 CCDS13624.1 IFRD1 NM_001007245 IGF1 CCDS9091.1 IGF2 CCDS7728.1 IGFBP7 CCDS3512.1 IGSF1 CCDS14629.1 IGSF10 CCDS3160.1 IGSF9 CCDS1190.1 IKBKE NM_014002 IL12RB2 CCDS638.1 IL17B CCDS4297.1 IL17RE CCDS2589.1 IL1F9 CCDS2108.1 IL1RL1 CCDS2057.1 IL3 CCDS4149.1 ILT7 CCDS12890.1 IMP4 CCDS2160.1 IMPDH1 NM_183243 INDO NM_002164 INSIG2 CCDS2122.1 IPO13 CCDS503.1 IPO8 CCDS8719.1 IQGAP2 NM_006633 IQWD1 CCDS1267.1 IRS1 CCDS2463.1 IRTA2 CCDS1165.1 IRX6 NM_024335 ISL1 NM_002202 ITGA4 NM_000885 ITGA7 CCDS8888.1 ITGAL NM_002209 ITGAX CCDS10711.1 ITIH5 NM_032817 ITLN1 CCDS1211.1 ITPKB CCDS1555.1 ITPR3 CCDS4783.1 IVNS1ABP CCDS1368.1 JMJD1A CCDS1990.1 JMJD1B NM_016604 JUNB CCDS12280.1 K0574_HUMAN ENST00000261275 KATNAL2 NM_031303 KBTBD3 CCDS8334.1 KBTBD4 CCDS7940.1 KCNA4 NM_002233 KCNA7 CCDS12755.1 KCNB2 CCDS6209.1 KCNC4 CCDS821.1 KCND2 CCDS5776.1 KCNG3 CCDS1809.1 KCNH1 CCDS1496.1 KCNH5 CCDS9756.1 KCNJ15 CCDS13656.1 KCNK1 CCDS1599.1 KCNK5 CCDS4841.1 KCNN1 NM_002248 KCNQ3 NM_004519 KCNQ4 CCDS456.1 KCTD7 CCDS5534.1 KCTD8 CCDS3467.1 KDELR2 CCDS5351.1 KDR CCDS3497.1 KEL NM_000420 KIAA0082 CCDS4835.1 KIAA0101 CCDS10193.1 KIAA0103 CCDS6309.1 KIAA0133 NM_014777 KIAA0143 NM_015137 KIAA0153 CCDS14047.1 KIAA0317 NM_001039479 KIAA0329 NM_014844 KIAA0350 NM_015226 KIAA0367 NM_015225 KIAA0404 NM_015104 KIAA0406 CCDS13300.1 KIAA0528 NM_014802 KIAA0649 CCDS6988.1 KIAA0652 CCDS7921.1 KIAA0664 NM_015229 KIAA0672 NM_014859 KIAA0690 CCDS7457.1 KIAA0701 NM_001006947 KIAA0703 NM_014861 KIAA0748 ENST00000316577 KIAA0759 CCDS9852.1 KIAA0774 NM_001033602 KIAA0802 CCDS11841.1 KIAA0831 NM_014924 KIAA0863 NM_014913 KIAA0980 NM_025176 KIAA1024 NM_015206 KIAA1033 NM_05275 KIAA1086 ENST00000262961 KIAA1109 ENST00000264501 KIAA1223 NM_020337 KIAA1274 NM_014431 KIAA1328 NM_020776 KIAA1377 NM_020802 KIAA1411 NM_020819 KIAA1441 CCDS992.1 KIAA1467 NM_020853 KIAA1505 NM_020879 KIAA1524 NM_020890 KIAA1576 NM_020927 KIAA1618 CCDS11772.1 KIAA1754L NM_178495 KIAA1804 CCDS1598.1 KIAA1862 NM_032534 KIAA1909 NM_052909 KIAA1946 NM_177454 KIAA1967 NM_021174 KIAA2022 NM_001008537 KIAA2026 NM_001017969 KIDINS220 NM_020738 KIFC2 CCDS6427.1 KIFC3 CCDS10789.1 KIRREL2 CCDS12479.1 KIRREL3 NM_032531 KLHDC5 NM_020782 KLHL10 NM_152467 KLHL4 CCDS14456.1 KLK9 CCDS12816.1 KLP1 CCDS12926.1 KLRG1 CCDS8599.1 KNTC1 NM_014708 KREMEN2 CCDS10484.1 KREMEN2 CCDS10483.1 KRT9 NM_000226 KRTAP12-3 NM_198697 KRTAP20-2 CCDS13604.1 KRTHA4 CCDS11390.1 KSR1 NM_014238 L1CAM CCDS14733.1 L3MBTL2 CCDS14011.1 LACE1 CCDS5067.1 LACRT CCDS8883.1 LAMA1 NM_005559 LAMA3 CCDS11880.1 LAMA4 NM_002290 LAMB3 CCDS1487.1 LAMP3 CCDS3242.1 LAP1B CCDS1335.1 LARGE CCDS13912.1 LARP5 NM_015155 LATS1 NM_004690 LATS2 CCDS9294.1 LAX CCDS1441.1 LBP CCDS13304.1 LCA10 NM_001039768 LCT CCDS2178.1 LDLRAD3 NM_174902 LEMD2 CCDS4785.1 LENG8 CCDS12894.1 LETM1 CCDS3355.1 LETMD1 CCDS8806.1 LIP8 CCDS11126.1 LIPM ENST00000282673 LMNB1 CCDS4140.1 LMX1A CCDS1247.1 LNX CCDS3492.1 LNX2 CCDS9323.1 LOC113655 CCDS6431.1 LOC124842 CCDS11283.1 LOC126248 CCDS12429.1 LOC131368 CCDS2947.1 LOC131873 ENST00000358511 LOC134145 NM_199133 LOC146562 CCDS10521.1 LOC158830 NM_001025265 LOC200312 NM_001017981 LOC221955 CCDS5350.1 LOC257106 CCDS1215.1 LOC283537 CCDS9332.1 LOC284912 CCDS13918.1 LOC284948 CCDS1976.1 LOC339977 NM_001024611 LOC374768 NM_199339 LOC387755 NM_001031853 LOC387856 NM_001013635 LOC388595 NM_001013641 LOC388969 NM_001013649 LOC391123 NM_001013661 LOC392617 ENST00000333066 LOC400707 NM_001013673 LOC441136 NM_001013719 LOC441233 NM_001013724 LOC442213 NM_001013732 LOC494115 NM_001008662 LOC51058 CCDS476.1 LOC54103 NM_017439 LOC54499 CCDS1251.1 LOC550631 NM_001017437 LOC63928 CCDS10617.1 LOC643866 NM_001039771 LOC648272 ENST00000343945 LOC651746 ENST00000296657 LOC651863 ENST00000333744 LOC90379 NM_138353 LOC90826 CCDS3771.1 LOC92154 NM_138383 LOC93349 NM_138402 LPAL2 ENST00000342479 LPHN1 CCDS12307.1 LPHN2 CCDS689.1 LPHN3 NM_015236 LPIN3 NM_022896 LPL CCDS6012.1 LRAT CCDS3789.1 LRCH1 NM_015116 LRFN5 CCDS9678.1 LRP1 CCDS8932.1 LRP10 CCDS9578.1 LRP1B CCDS2182.1 LRP2 CCDS2232.1 LRRC16 NM_017640 LRRC4 CCDS5799.1 LRRC4B ENST00000253728 LRRC7 CCDS645.1 LRRIQ1 NM_032165 LRRK1 NM_024652 LRRN1 NM_020873 LRRN3 CCDS5754.1 LRRN5 CCDS1448.1 LTB4R2 CCDS9624.1 LTBP1 NM_000627 LTBP3 CCDS8103.1 LTBP4 NM_003573 LTK CCDS10077.1 LUC7L CCDS10401.1 LY6K CCDS6385.1 LYNX1 ENST00000317543 LYPLA1 CCDS6157.1 LYRIC CCDS6274.1 LYST NM_000081 LYZL4 CCDS2697.1 LZTR2 NM_033127 M160 CCDS8577.1 MACF1 CCDS435.1 MAEA NM_001017405 MAGEA4 CCDS14702.1 MAGEB10 NM_182506 MAGEC1 NM_005462 MAGEH1 CCDS14369.1 MAGI-3 CCDS859.1 MAK10 CCDS6673.1 MALT1 CCDS11967.1 MAMDC2 CCDS6631.1 MAN1B1 CCDS7029.1 MAN2A1 NM_002372 MAN2B1 NM_000528 MAP1B CCDS4012.1 MAP3K11 CCDS8107.1 MAP3K14 NM_003954 MAP3K8 CCDS7166.1 MAP3K9 NM_033141 MAP4K4 NM_004834 MAP7D3 ENST00000218318 MARCO CCDS2124.1 MARK3 NM_002376 MARS CCDS8942.1 MARS2 NM_138395 MASS1 NM_032119 MAST4 ENST00000261569 MATN1 CCDS336.1 MBD1 CCDS11941.1 MBNL1 CCDS3163.1 MCCC1 CCDS3241.1 MCF2L ENST00000261963 MCFD2 NM_139279 MCM10 CCDS7095.1 MCPH1 NM_024596 MDGA1 NM_153487 MDH2 CCDS5581.1 MEA CCDS4879.1 MED12 NM_005120 MEFV CCDS10498.1 MEN1 CCDS8083.1 METTL5 NM_014168 MGAM NM_004668 MGC16635 CCDS14097.1 MGC19764 NM_144975 MGC20419 CCDS562.1 MGC20741 CCDS4861.1 MGC21830 CCDS10463.1 MGC24039 NM_144973 MGC2655 CCDS10491.1 MGC26598 CCDS9036.1 MGC26818 CCDS44.1 MGC27016 CCDS3790.1 MGC29814 CCDS11742.1 MGC29875 CCDS1493.1 MGC33367 CCDS10738.1 MGC33414 CCDS279.1 MGC33486 CCDS8133.1 MGC33889 CCDS14216.1 MGC34647 CCDS10895.1 MGC35118 CCDS10046.1 MGC35194 CCDS147.1 MGC35366 CCDS9057.1 MGC39581 CCDS12149.1 MGC42174 NM_152383 MGC4251 CCDS11474.1 MGC4268 CCDS2152.1 MGC45562 CCDS11371.1 MGC45780 CCDS6064.1 MGC47869 CCDS8667.1 MHC2TA CCDS10544.1 MIA3 ENST00000320831 MICAL-L2 CCDS5324.1 MINK1 NM_170663 MIPEP CCDS9303.1 MIR16 CCDS10578.1 MKI67 CCDS7659.1 MLL NM_005933 MLL3 CCDS5931.1 MLL4 NM_014727 MLLT4 CCDS5303.1 MLLT7 NM_005938 MME CCDS3172.1 MMP10 CCDS8321.1 MMP16 CCDS6246.1 MOCS1 CCDS4845.1 MON2 NM_015026 MPDU1 CCDS11115.1 MPDZ NM_003829 MPP1 CCDS14762.1 MPZ CCDS1229.1 MRC2 CCDS11634.1 MRGX1 CCDS7846.1 MRPL13 CCDS6332.1 MRPL16 CCDS7976.1 MRPL37 ENST00000329505 MRPL44 CCDS2459.1 MRPL46 CCDS10341.1 MRPL55 CCDS1567.1 MRPS5 CCDS2010.1 MRPS7 CCDS11718.1 MRVI1 NM_006069 MS4A7 CCDS7985.1 MSI2 CCDS11596.1 MSL2L1 NM_018133 MSRB3 CCDS8973.1 MTA1 NM_004689 MTHFD2L NM_001004346 MTNR1B CCDS8290.1 MTP CCDS3651.1 MTR CCDS1614.1 MTX2 CCDS2272.1 MUC15 CCDS7859.1 MUC16 NM_024690 MUC5AC ENST00000349637 MUC7 CCDS3541.1 MVP CCDS10656.1 MYBPC3 NM_000256 MYBPHL NM_001010985 MYF6 CCDS9019.1 MYH14 NM_024729 MYH15 ENST00000273353 MYH3 CCDS11157.1 MYH4 CCDS11154.1 MYO15A NM_016239 MYO18B NM_032608 MYO1B CCDS2311.1 MYO1D NM_015194 MYO1E NM_004998 MYO3A CCDS7148.1 MYO3B NM_138995 MYO5A NM_000259 MYO5C NM_018728 MYO9B NM_004145 MYOCD CCDS11163.1 MYOM1 NM_003803 MYOM2 CCDS5957.1 MYR8 NM_015011 MYRIP CCDS2689.1 MYST3 CCDS6124.1 MYT1L NM_015025 NAGA CCDS14030.1 NALP1 NM_014922 NALP11 CCDS12935.1 NALP7 CCDS12912.1 NAPSB ENST00000253720 NARG1L CCDS9379.1 NAV1 CCDS1414.1 NCBP1 CCDS6728.1 NCKAP1L NM_005337 NCOA5 CCDS13392.1 NCOA6 CCDS13241.1 NDUFA11 CCDS12155.1 NDUFB2 CCDS5862.1 NDUFS6 CCDS3866.1 NEB NM_004543 NEIL3 CCDS3828.1 NEUROG2 CCDS3698.1 NF1 CCDS11264.1 NFATC3 CCDS10862.1 NFATC4 CCDS9629.1 NGEF CCDS2500.1 NHS CCDS14181.1 NIF3L1BP1 CCDS2900.1 NIN NM_182944 NISCH NM_007184 NKG7 CCDS12830.1 NKRF NM_017544 NKX2-5 CCDS4387.1 NLGN1 CCDS3222.1 NLGN2 CCDS11103.1 NLN CCDS3989.1 NM_001080470.1 ENST00000271263 NMBR CCDS5196.1 NMUR1 CCDS2486.1 NNT CCDS3949.1 NOD3 NM_178844 NOR1 CCDS409.1 NOS3 CCDS5912.1 NOTCH1 NM_017617 NOTCH2 CCDS908.1 NOTCH3 CCDS12326.1 NOTCH4 NM_004557 NOX4 CCDS8285.1 NP_001073909.1 ENST00000327928 NP_001073931.1 ENST00000341689 NP_001073940.1 ENST00000292357 NP_001073948.1 ENST00000296794 NP_001073961.1 ENST00000219301 NP_001073971.1 ENST00000266524 NP_001074294.1 ENST00000342607 NPC1L1 CCDS5491.1 NPL CCDS1350.1 NPLOC4 NM_017921 NPPA CCDS139.1 NPR3 NM_000908 NPTXR NM_014293 NR_002781.1 ENST00000246203 NR2E1 CCDS5063.1 NRAP CCDS7578.1 NRBP2 NM_178564 NRK NM_198465 NRP1 CCDS7177.1 NRP2 CCDS2364.1 NRXN2 CCDS8077.1 NS3TP2 CCDS4136.1 NT5E CCDS5002.1 NTN2L CCDS10469.1 NTRK3 CCDS10340.1 NUAK1 NM_014840 NUP160 NM_015231 NUP188 NM_015354 NUP205 NM_015135 NUP210L NM_207308 NUP98 CCDS7746.1 NURIT CCDS9399.1 NXF3 CCDS14503.1 NXF5 CCDS14491.1 NXPH1 NM_152745 OAS3 NM_006187 OBSCN CCDS1570.1 ODZ2 ENST00000314238 OLIG2 CCDS13620.1 OPRD1 CCDS329.1 OPRL1 CCDS13556.1 OR10G3 NM_001005465 OR10G4 NM_001004462 OR10H2 CCDS12333.1 OR10P1 NM_206899 OR10T2 NM_001004475 OR13J1 NM_001004487 OR1L8 NM_001004454 OR2A12 NM_001004135 OR2AG1 NM_001004489 OR2AG2 NM_001004490 OR2D2 NM_003700 OR2G3 NM_001001914 OR2L13 CCDS1637.1 OR2L2 NM_001004686 OR2S2 CCDS6596.1 OR2T4 NM_001004696 OR2V2 CCDS4461.1 OR2Y1 NM_001001657 OR2Z1 NM_001004699 OR3A1 CCDS11023.1 OR4A5 NM_001005272 OR4L1 NM_001004717 OR4N2 NM_001004723 OR4P4 NM_001004124 OR52A5 NM_001005160 OR52B2 NM_001004052 OR52D1 NM_001005163 OR52E6 NM_001005167 OR52I1 NM_001005169 OR52N4 NM_001005175 OR56A4 NM_001005179 OR56B1 NM_001005180 OR56B4 NM_001005181 OR5A1 NM_001004728 OR5AP2 NM_001002925 OR5AU1 NM_001004731 OR5B17 ENST00000357377 OR5BF1 NM_001001918 OR5D14 NM_001004735 OR5K4 NM_001005517 OR5M1 ENST00000303005 OR5M8 NM_001005282 OR5M9 NM_001004743 OR6C74 NM_001005490 OR6K3 NM_001005327 OR6W1P ENST00000340373 OR7A5 CCDS12318.1 OR7D4 NM_001005191 OR8D2 NM_001002918 OR8K3 NM_001005202 OR9K2 NM_001005243 OR9Q2 NM_001005283 OSAP NM_032623 OSBPL2 CCDS13494.1 OSBPL5 NM_145638 OSBPL9 CCDS558.1 OSR2 NM_053001 OSTM1 CCDS5062.1 OTOF CCDS1725.1 OTOG ENST00000342528 OTOR CCDS13124.1 OTUD1 ENST00000298035 OVCH1 NM_183378 OVOL1 CCDS8112.1 OXA1L CCDS9573.1 p44S10 CCDS2901.1 PADI2 CCDS177.1 PAPLN NM_173462 PAPOLG CCDS1863.1 PAPPA2 NM_020318 PARC CCDS4890.1 PARP11 CCDS8523.1 PAX9 CCDS9662.1 PCAF CCDS2634.1 PCDH11X CCDS14463.1 PCDHA10 NM_031859 PCDHA13 CCDS4240.1 PCDHB7 CCDS4249.1 PCDHGA4 NM_032053 PCDHGA9 NM_032089 PCDHGB7 NM_032101 PCDHGC4 CCDS4260.1 PCDHGC4 CCDS4261.1 PCDHGC4 CCDS4263.1 PCGF2 NM_007144 PCNXL2 ENST00000344698 PCSK2 CCDS13125.1 PCYOX1 CCDS1902.1 PDCD10 CCDS3202.1 PDCD11 NM_014976 PDE1C CCDS5437.1 PDE4A CCDS12238.1 PDE4B CCDS632.1 PDE4C CCDS12373.1 PDE4D NM_006203 PDGFB CCDS13987.1 PDGFRA CCDS3495.1 PDGFRB CCDS4303.1 PDHA2 CCDS3644.1 PDHB CCDS2890.1 PDIA2 NM_006849 PDK1 CCDS2250.1 PDLIM4 CCDS4152.1 PDZD2 NM_178140 PDZD7 NM_024895 PEG10 ENST00000362013 PELP1 NM_014389 PENK CCDS6168.1 PERQ1 NM_022574 PEX1 CCDS5627.1 PEX10 CCDS41.1 PFAS CCDS11136.1 PFKFB3 CCDS7078.1 PGAP1 CCDS2318.1 PGBD5 CCDS1583.1 PHC3 NM_024947 PHEMX CCDS7733.1 PHF2 ENST00000298216 PHF21A NM_016621 PHIP CCDS4987.1 PHKA2 CCDS14190.1 PHLPP NM_194449 PHLPPL NM_015020 PHOX2B CCDS3463.1 PIGN NM_176787 PIGQ CCDS10411.1 PIGR CCDS1474.1 PIK3C2G NM_004570 PIK3CA NM_006218 PIK3CG CCDS5739.1 PIK3R1 CCDS3993.1 PIK3R4 CCDS3067.1 PIK3R5 CCDS11147.1 PIP5K1A CCDS990.1 PIP5K3 CCDS2382.1 PISD CCDS13899.1 PITPNM1 NM_004910 PITPNM2 CCDS9242.1 PITPNM3 CCDS11076.1 PIWIL3 NM_001008496 PKD1 NM_000296 PKD1L2 NM_182740 PKHD1 CCDS4935.1 PKHD1L1 NM_177531 PKIA CCDS6222.1 PLA1A CCDS2991.1 PLCH2 NM_014638 PLCXD3 NM_001005473 PLD2 CCDS11057.1 PLEC1 NM_201378 PLEKHA4 CCDS12737.1 PLEKHH2 CCDS1812.1 PLIN CCDS10353.1 PLSCR3 NM_020360 PLXDC2 CCDS7132.1 PLXNA3 CCDS14752.1 PLXNB2 ENST00000359337 PLXNC1 CCDS9049.1 PMS1 CCDS2302.1 PMS2L4 ENST00000275546 PNLIP CCDS7594.1 PNOC CCDS6066.1 PODXL2 CCDS3044.1 POLD1 CCDS12795.1 POLE CCDS9278.1 POLG2 NM_007215 POLM NM_013284 POLR3B CCDS9105.1 POLR3E CCDS10605.1 POPDC2 CCDS2992.1 POR CCDS5579.1 PORCN CCDS14296.1 POT1 CCDS5793.1 POU1F1 CCDS2919.1 POU2F1 CCDS1259.1 POU6F2 NM_007252 PPAP2C CCDS12023.1 PPARA NM_001001930 PPBP CCDS3563.1 PPEF2 NM_006239 PPIG CCDS2235.1 PPL CCDS10526.1 PPM2C CCDS6259.1 PPP1CC CCDS9150.1 PPP1R12A NM_002480 PPP1R12C CCDS12916.1 PPP2CZ CCDS855.1 PPP2R2C CCDS3387.1 PPRC1 CCDS7529.1 PRCC CCDS1157.1 PRDM16 NM_199454 PRDM5 CCDS3716.1 PRELP CCDS1438.1 PRIC285 CCDS13527.1 PRKCBP1 CCDS13404.1 PRKCZ CCDS37.1 PRKDC NM_006904 PRKG2 CCDS3589.1 PRKRA CCDS2279.1 PRO1853 CCDS1788.1 PRO1855 CCDS11566.1 PROM1 NM_006017 PROSC CCDS6096.1 PRPF18 CCDS7100.1 PRR12 ENST00000246798 PRSS16 CCDS4623.1 PRSS22 CCDS10481.1 PSF1 NM_021067 PSIP1 CCDS6479.1 PSMD8 CCDS12515.1 PSRC2 NM_144982 PTAR1 ENST00000340434 PTCH2 CCDS516.1 PTEN NM_000314 PTGDR CCDS9707.1 PTGFR CCDS686.1 PTGS2 CCDS1371.1 PTPLA CCDS7121.1 PTPN23 CCDS2754.1 PTPRF CCDS489.1 PTPRK CCDS5137.1 PTPRM CCDS11840.1 PTPRS CCDS12139.1 PTPRU CCDS334.1 PTX3 CCDS3180.1 PUM1 CCDS338.1 PYGB CCDS13171.1 Q13034_HUMAN ENST00000225928 Q4VXG5_HUMAN ENST00000327794 Q4VXG5_HUMAN ENST00000331811 Q5JX50_HUMAN ENST00000325076 Q5JYU7_HUMAN ENST00000333418 Q5T740_HUMAN ENST00000343319 Q5W0A0_HUMAN ENST00000298738 Q68CJ6_HUMAN ENST00000341513 Q61EE8_HUMAN ENST00000354872 Q6PK04_HUMAN ENST00000329214 Q6RGF6_HUMAN ENST00000359144 Q6ZRB0_HUMAN ENST00000297487 Q6ZSY1_HUMAN ENST00000320930 Q6ZT40_HUMAN ENST00000296564 Q6ZUG5_HUMAN ENST00000344062 Q6ZV46_HUMAN ENST00000341696 Q76B61_HUMAN ENST00000360022 Q86U37_HUMAN ENST00000335192 Q86XQ1_HUMAN ENST00000261673 Q86YU6_HUMAN ENST00000330768 Q8IUR1_HUMAN ENST00000327506 Q8N1R6_HUMAN ENST00000331014 Q8N646_HUMAN ENST00000359720 Q8N800_HUMAN ENST00000322516 Q8N822_HUMAN ENST00000317280 Q8N8C3_HUMAN ENST00000319889 Q8N8K0_HUMAN ENST00000301807 Q8N9H1_HUMAN ENST00000359503 Q8NBE0_HUMAN ENST00000297801 Q8NDH2_HUMAN ENST00000322527 Q8NGK8_HUMAN ENST00000334020 Q8NGL5_HUMAN ENST00000328673 Q8NH06_HUMAN ENST00000324144 Q8NHB0_HUMAN ENST00000315712 Q8TBR1_HUMAN ENST00000354206 Q96CH6_HUMAN ENST00000329920 Q96CK5_HUMAN ENST00000273582 Q96DR3_HUMAN ENST00000324748 Q96FF7_HUMAN ENST00000269720 Q96NE0_HUMAN ENST00000329922 Q96NL2_HUMAN ENST00000272907 Q96PS2_HUMAN ENST00000326978 Q9H030_HUMAN ENST00000237449 Q9H6A9_HUMAN ENST00000309024 Q9H800_HUMAN ENST00000357106 Q9H8D1_HUMAN ENST00000360549 Q9HAC4_HUMAN ENST00000206466 Q9P1M5_HUMAN ENST00000303007 Q9ULE4_HUMAN ENST00000265018 Q9Y6V0-3 ENST00000333891 QPCT CCDS1790.1 QRICH2 NM_032134 QSCN6 CCDS1337.1 QSER1 NM_024774 QTRTD1 NM_024638 RAB36 CCDS13805.1 RAB3C CCDS3976.1 RAB3GAP2 NM_012414 RAB3IL1 CCDS8014.1 RAC2 CCDS13945.1 RAD23A CCDS12289.1 RAD51L3 CCDS11287.1 RAD52 CCDS8507.1 RAFTLIN NM_015150 RAI1 CCDS11188.1 RALBP1 CCDS11845.1 RANBP17 NM_022897 RANP1 ENST00000333828 RAP140 CCDS2877.1 RAPGEF4 NM_007023 RAPGEF6 NM_016340 RAPGEFL1 CCDS11363.1 RAPH1 CCDS2359.1 RARSL CCDS5011.1 RASGRF1 CCDS10309.1 RASGRF2 CCDS4052.1 RASL11B CCDS3490.1 RAX CCDS11972.1 RB1 NM_000321 RBM14 CCDS8147.1 RBM19 CCDS9172.1 RBM21 CCDS8021.1 RBM25 NM_021239 RBM27 ENST00000265271 RBM34 ENST00000362051 RBMS3 NM_001003792 RBP3 CCDS7218.1 RBPSUH CCDS3436.1 RC74 NM_018250 RCD-8 CCDS10849.1 RDHE2 CCDS6167.1 RDS CCDS4871.1 REG1B CCDS1963.1 REN NM_000537 REPS2 CCDS14180.1 RET CCDS7200.1 RFC2 CCDS5567.1 RFNG NM_002917 RFX3 CCDS6450.1 RGS22 NM_015668 RGSL1 CCDS1346.1 RHOT1 NM_001033568 RICTOR NM_152756 RIMBP2 NM_015347 RIMS2 NM_014677 RIMS4 CCDS13338.1 RIPK4 CCDS13675.1 RLBP1 NM_000326 RLTPR NM_001013838 RNASEH2A CCDS12282.1 RNF103 NM_005667 RNF127 CCDS14575.1 RNF128 CCDS14521.1 RNF19 CCDS6286.1 RNF25 CCDS2420.1 RNF40 CCDS10691.1 RNPC2 CCDS13265.1 ROBO3 NM_022370 ROCK1 CCDS11870.1 ROM1 CCDS8024.1 ROS1 CCDS5116.1 RoXaN CCDS14013.1 RP1L1 NM_178857 RPL11 CCDS238.1 RPS14 CCDS4307.1 RPS6KA2 CCDS5294.1 RPS6KB2 NM_003952 RPUSD3 CCDS2586.1 RRAGD CCDS5022.1 RSHL1 CCDS12675.1 RSU1 CCDS7112.1 RTN1 CCDS9740.1 RTTN NM_173630 RUNX1 CCDS13639.1 RUNX1T1 CCDS6256.1 RWDD1 NM_001007464 RYR2 NM_001035 RYR3 NM_001036 SALL3 CCDS12013.1 SAMD11 ENST00000294573 SAMD9 NM_017654 SAPS2 NM_014678 SARG CCDS1475.1 SARS CCDS795.1 SASH1 CCDS5212.1 SCHIP1 CCDS3186.1 SCN1B CCDS12441.1 SCN3A NM_006922 SCN3B CCDS8442.1 SCN5A NM_000335 SCN9A NM_002977 SCRIB CCDS6411.1 SCUBE1 CCDS14048.1 SDC3 NM_014654 SDR-O CCDS8926.1 SEC24C CCDS7332.1 SELO NM_031454 SEMA5A CCDS3875.1 SEMA5B CCDS3019.1 SEMA7A CCDS10262.1 SEN2L CCDS2611.1 SENP3 NM_015670 SEPT2 CCDS2548.1 SERPINA12 CCDS9926.1 SERPINA9 NM_175739 SERPINB3 CCDS11987.1 SERPINB7 CCDS11988.1 SERPINE2 CCDS2460.1 SERPING1 CCDS7962.1 SET7 CCDS3748.1 SETDB2 CCDS9417.1 SEZ6 NM_178860 SEZ6L CCDS13833.1 SFI1 NM_001007467 SFMBT2 NM_001029880 SFRP2 NM_003013 SFTPB CCDS1983.1 SG223_HUMAN ENST00000330777 SGCZ CCDS5992.1 SGK2 CCDS13320.1 SGPP1 CCDS9760.1 SGPP2 CCDS2453.1 SGSH CCDS11770.1 SH3BP1 CCDS13952.1 SH3BP2 NM_003023 SH3GL3 CCDS10325.1 SHANK2 CCDS8198.1 SHANK3 ENST00000262795 SHB NM_003028 SHE NM_001010846 SHMT2 CCDS8934.1 SIGLEC11 CCDS12790.1 SIGLEC5 NM_003830 SIGLEC8 NM_014442 SIM2 CCDS13646.1 SIPA1L2 NM_020808 SIPA1L3 NM_015073 SKIV2L CCDS4731.1 SKP2 CCDS3915.1 SLC10A4 CCDS3482.1 SLC11A1 CCDS2415.1 SLC12A1 CCDS10129.1 SLC12A5 CCDS13391.1 SLC14A1 CCDS11925.1 SLC14A2 CCDS11924.1 SLC16A5 CCDS11713.1 SLC1A2 NM_004171 SLC22A11 CCDS8074.1 SLC22A18 CCDS7740.1 SLC22A3 CCDS5277.1 SLC24A6 NM_024959 SLC25A13 CCDS5645.1 SLC26A4 CCDS5746.1 SLC2A1 CCDS477.1 SLC30A1 CCDS1499.1 SLC30A5 CCDS3996.1 SLC30A9 CCDS3465.1 SLC35B2 NM_178148 SLC35D3 NM_001008783 SLC35F2 NM_017515 SLC38A1 NM_030674 SLC38A4 CCDS8750.1 SLC38A6 CCDS9751.1 SLC39A2 CCDS9563.1 SLC43A3 CCDS7956.1 SLC4A1 CCDS11481.1 SLC4A5 CCDS1936.1 SLC4A7 NM_003615 SLC5A5 CCDS12368.1 SLC5A7 CCDS2074.1 SLC7A10 CCDS12431.1 SLC7A13 NM_138817 SLC7A14 NM_020949 SLC7A6 NM_003983 SLC8A1 CCDS1806.1 SLC9A1 CCDS295.1 SLC9A2 CCDS2062.1 SLC9A3R2 NM_004785 SLC9A4 NM_001011552 SLCO1B1 CCDS8685.1 SLCO2A1 CCDS3084.1 SLCO4C1 NM_180991 SLCO6A1 NM_173488 SLIT2 CCDS3426.1 SLITRK1 CCDS9464.1 SLITRK5 CCDS9465.1 SLITRK6 ENST00000313206 SMARCA2 NM_003070 SMARCA4 CCDS12253.1 SMARCC2 CCDS8907.1 SMC5L1 CCDS6632.1 SMCR8 CCDS11195.1 SMF_HUMAN ENST00000261804 SN CCDS13060.1 SNED1 ENST00000310397 SNRPA CCDS12565.1 SNX13 NM_015132 SNX27 CCDS1001.1 SNX4 CCDS3032.1 SOCS5 CCDS1830.1 SOHLH1 NM_001012415 SORCS2 NM_020777 SORCS3 CCDS7558.1 SORL1 CCDS8436.1 SOS1 CCDS1802.1 SOSTDC1 CCDS5360.1 SOX13 NM_005686 SOX30 CCDS4339.1 SOX8 CCDS10428.1 SP100 CCDS2477.1 SPACA4 CCDS12725.1 SPAG1 NM_003114 SPAG5 NM_006461 SPAG7 NM_004890 SPATA1 CCDS697.1 SPATA2 CCDS13422.1 SPATC1 CCDS6413.1 Spc25 CCDS2229.1 SPEG ENST00000265327 SPEN CCDS164.1 SPG3A CCDS9700.1 SPI1 CCDS7933.1 SPIN3 NM_001010862 SPIRE2 NM_032451 SPN CCDS10650.1 SPOCK3 NM_016950 SPON2 CCDS3347.1 SPRED2 NM_181784 SPTB NM_001024858 SPTBN1 NM_178313 SPTBN2 CCDS8150.1 SPTBN4 CCDS12559.1 SPTBN5 NM_016642 SREBF2 CCDS14023.1 SRGAP1 CCDS8967.1 SRPK2 CCDS5735.1 SRRM2 NM_016333 SSFA2 CCDS2284.1 ST14 CCDS8487.1 ST8SIA4 CCDS4091.1 STAB1 NM_015136 STAP2 CCDS12128.1 STIM2 CCDS3440.1 STK33 CCDS7789.1 STK39 NM_013233 STRA6 CCDS10261.1 STS CCDS14127.1 STS-1 NM_032873 STX11 CCDS5205.1 STX12 CCDS310.1 STXBP2 CCDS12181.1 STXBP3 CCDS790.1 STYK1 CCDS8629.1 SUCLA2 CCDS9406.1 SUCLG2 NM_003848 SULT6B1 NM_001032377 SUNC1 NM_152782 SUSD5 ENST00000309558 SV2B CCDS10370.1 SWAP70 NM_015055 SYDE2 ENST00000234668 SYN2 NM_133625 SYNE1 CCDS5236.1 SYNE1 CCDS5237.1 SYNE2 CCDS9761.1 SYT15 NM_181519 SYT16 NM_031914 SYT6 CCDS871.1 TAAR9 ENST00000340640 TACC2 CCDS7626.1 TACC3 CCDS3352.1 TAF1L NM_153809 TAF4B ENST00000269142 TAF6 CCDS5686.1 TANC1 NM_033394 TAOK1 NM_020791 TARBP2 CCDS8861.1 TAS1R2 CCDS187.1 TAS2R3 CCDS5867.1 TBC1D20 CCDS13002.1 TBC1D4 NM_014832 TBCD NM_001033052 TBX20 CCDS5445.1 TBX22 CCDS14445.1 TCF7L1 CCDS1971.1 TCF8 CCDS7169.1 TCHH ENST00000290632 TCN2 CCDS13881.1 TDRD5 CCDS1332.1 TDRD9 CCDS9987.1 TEAD2 CCDS12761.1 TEPP CCDS10790.1 TERF2IP NM_018975 TFE3 CCDS14315.1 TGFBRAP1 CCDS2067.1 TGM1 CCDS9622.1 TGM5 NM_004245 THAP9 CCDS3598.1 THES1 NM_003246 THEA CCDS592.1 THOP1 CCDS12095.1 THRAP3 ENST00000354618 THSD7B ENST00000272643 TIMP2 CCDS11758.1 TINAG CCDS4955.1 TJP3 NM_014428 TLL1 CCDS3811.1 TLN1 NM_006289 TLX3 NM_021025 TM4SF14 CCDS7369.1 TM4SF3 CCDS8999.1 TM9SF4 CCDS13196.1 TMED1 CCDS12249.1 TMEM131 ENST00000186436 TMEM132C ENST00000315208 TMEM16B NM_020373 TMEM16C NM_031418 TMEM16E NM_213599 TMEM16G NM_001001891 TMEM16J NM_001012302 TMEM38A CCDS12349.1 TMEM46 NM_001007538 TMEM63B NM_018426 TMEM8 CCDS10407.1 TMPRSS2 NM_005656 TMPRSS4 NM_019894 TNC CCDS6811.1 TNFAIP2 CCDS9979.1 TNFSF18 CCDS1305.1 TNFSF4 CCDS1306.1 TNFSF9 CCDS12169.1 TNIP1 NM_006058 TNIP2 CCDS3362.1 TNK1 NM_003985 TNMD CCDS14469.1 TNN NM_022093 TNPO1 CCDS4016.1 TNR CCDS1318.1 TNRC15 NM_015575 TNRC4 CCDS1002.1 TNRC6C NM_018996 TOE1 CCDS521.1 TOP2A NM_001067 TOR1A CCDS6930.1 TOSO CCDS1473.1 TP53 CCDS11118.1 TPH2 NM_173353 TPR NM_003292 TPST2 CCDS13839.1 TRAM1L1 CCDS3707.1 TRAPPC3 CCDS404.1 TREML2 CCDS4853.1 TREML3 ENST00000332842 TRIM14 CCDS6734.1 TRIM42 CCDS3113.1 TRIM45 CCDS893.1 TRIM46 CCDS1097.1 TRIM55 CCDS6186.1 TRIM56 NM_030961 TRIM58 CCDS1636.1 TRIO CCDS3883.1 TRIOBP NM_007032 TRIP12 NM_004238 TRIP6 CCDS5708.1 TRMT5 NM_020810 TRPC4AP CCDS13246.1 TRPC6 CCDS8311.1 TRPM2 CCDS13710.1 TRPM3 CCDS6634.1 TRPM4 NM_017636 TRPM5 NM_014555 TRPM6 CCDS6647.1 TRPM7 NM_017672 TRPV5 CCDS5875.1 TRRAP CCDS5659.1 TSAP6 CCDS2125.1 TSC2 CCDS10458.1 TSCOT CCDS6786.1 TSGA10 CCDS2037.1 TTC12 CCDS8360.1 TTC18 CCDS7324.1 TTC6 NM_001007795 TTLL2 CCDS5301.1 TTLL5 NM_015072 TTN NM_133378 TTN NM_133432 TUBGCP3 CCDS9525.1 TUBGCP6 CCDS14087.1 TULP1 CCDS4807.1 TXNDC3 CCDS5452.1 TYR CCDS8284.1 UBAP2L CCDS1063.1 UBE2G2 CCDS13714.1 UCHL1 CCDS3462.1 UGCGL2 CCDS9480.1 UGDH CCDS3455.1 UGT1A6 CCDS2510.1 ULK1 CCDS9274.1 UNQ2446 CCDS10850.1 UNQ3030 CCDS3319.1 UNQ689 CCDS3542.1 UPK3B CCDS5588.1 URB1 ENST00000270201 USH2A CCDS1516.1 USP11 CCDS14277.1 USP26 CCDS14635.1 USP8 CCDS10137.1 VANGL1 CCDS883.1 VCAM1 CCDS773.1 VCIP135 CCDS6192.1 VCL CCDS7340.1 VDP NM_003715 VDR CCDS8757.1 VGCNL1 CCDS9498.1 VGLL2 CCDS5115.1 VIPR2 CCDS5950.1 VMD2 NM_004183 VN2R1P ENST00000312652 VPS11 NM_021729 VPS13A CCDS6655.1 VPS24 NM_001005753 VPS41 CCDS5457.1 VPS45A CCDS944.1 VSIG2 CCDS8452.1 VWF CCDS8539.1 WBSCR17 CCDS5540.1 WBSCR27 CCDS5561.1 WDFY3 CCDS3609.1 WDR21 CCDS9809.1 WDR22 NM_003861 WDR24 CCDS10420.1 WDR27 NM_182552 WDR32 CCDS6613.1 WDR34 CCDS6906.1 WDR42B ENST00000329763 WDR52 CCDS2972.1 WDR6 CCDS2782.1 WDR70 NM_018034 WDTC1 CCDS296.1 WEE1 CCDS7800.1 WFS1 CCDS3386.1 WNK1 CCDS8506.1 WNK2 CCDS6704.1 WNT9A NM_003395 XAB2 NM_020196 XDH CCDS1775.1 XPO1 NM_003400 XPO7 NM_015024 XR_016172.1 ENST00000355015 XR_017335.1 ENST00000314295 YN004_HUMAN ENST00000281581 YTHDC2 CCDS4113.1 YWHAH CCDS13901.1 ZAN NM_173059 ZBTB16 CCDS8367.1 ZBTB24 NM_014797 ZBTB4 CCDS11107.1 ZBTB9 NM_006772 ZC3H6 NM_198581 ZFPM1 NM_153813 ZFYVE9 CCDS563.1 ZIC1 CCDS3136.1 ZIK1 NM_001010879 ZMAT4 NM_024645 ZNF10 CCDS9283.1 ZNF160 CCDS12859.1 ZNF17 NM_006959 ZNF18 NM_144680 ZNF183L1 CCDS9486.1 ZNF189 CCDS6754.1 ZNF25 CCDS7195.1 ZNF286 CCDS11172.1 ZNF294 NM_015565 ZNF295 CCDS13678.1 ZNF30 NM_194325 ZNF31 NM_145238 ZNF313 NM_018683 ZNF318 CCDS4895.1 ZNF333 CCDS12316.1 ZNF339 CCDS13132.1 ZNF343 CCDS13028.1 ZNF358 NM_018083 ZNF366 CCDS4015.1 ZNF406 NM_001029939 ZNF440L NM_001012753 ZNF473 NM_015428 ZNF487 ENST00000315429 ZNF496 CCDS1631.1 ZNF497 CCDS12977.1 ZNF507 NM_014910 ZNF545 CCDS12493.1 ZNF547 NM_173631 ZNF558 CCDS12208.1 ZNF585A CCDS12499.1 ZNF628 NM_033113 ZNF67 ENST00000323012 ZNF79 CCDS6871.1 ZP2 CCDS10596.1 ZSCAN2 CCDS10329.1 ZSWIM4 NM_023072 ZW10 CCDS8363.1 Note: Gene symbols are standard symbols assigned by Entrz Gene (http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene). Accession IDs “NM_XXXX” are uniquely assigned to each gene by National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/sites/entrez?db=nuccore). Accession IDs “CCDSXXXX” are uniquely assigned to individual genes by National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/CCDS/). Accession IDs “ENSTXXXXXXXXXXX” are uniquely assigned to individual genes by Ensembl (http://www.ensembl.org/index.html).

TABLE 13 Genes containing somatic mutations in pancreatic cancer adapted from the paper by Jones et. al. (Jones et al., 2008). Gene Symbol Accession ID 7h3 CCDS12324.1 AARS NM_001605 ABCA1 CCDS6762.1 ABCA12 NM_015657 ABCA7 CCDS12055.1 ABCB5 CCDS5371.1 ABCD2 CCDS8734.1 ABLIM2 NM_032432 ACACB NM_001093 ACD CCDS10842.1 ACE CCDS11637.1 ACOT9 NM_001033583 ACTL7B CCDS6771.1 ADA CCDS13335.1 ADAM11 CCDS11486.1 ADAM12 CCDS7653.1 ADAM19 CCDS4338.1 ADAM21 CCDS9804.1 ADAMTS10 CCDS12206.1 ADAMTS15 CCDS8488.1 ADAMTS16 NM_139056 ADAMTS18 CCDS10926.1 ADAMTS2 CCDS4444.1 ADAMTS20 NM_175851 ADAMTS20 NM_025003 ADAMTS5 CCDS13579.1 ADAMTSL3 CCDS10326.1 ADCY2 CCDS3872.1 ADCY4 CCDS9627.1 ADD2 CCDS1906.1 ADPRHL2 CCDS402.1 AFF3 NM_001025108 AHNAK NM_024060 AHNAK NM_001620 AHR CCDS5366.1 AICDA NM_020661 AIM2 CCDS1181.1 AK3 CCDS629.1 AKAP12 CCDS5229.1 ALDH18A1 CCDS7443.1 ALDH1A3 CCDS10389.1 ALDH3A1 CCDS11212.1 ALDH3B1 NM_000694 ALDH8A1 CCDS5171.1 ALG8 CCDS8258.1 ALMS1 NM_015120 ALOX5 CCDS7212.1 AMIGO3 NM_198722 ANAPC4 CCDS3434.1 ANK3 CCDS7258.1 ANKAR ENST00000313581 ANKRD27 NM_032139 ANKRD6 NM_014942 ANKRD9 CCDS9973.1 ANXA13 NM_001003954 AOX1 NM_001159 AP3B2 NM_004644 APC2 CCDS12068.1 APG4A CCDS14538.1 APOB CCDS1703.1 APRIN NM_015032 APXL2 CCDS4161.1 AQP8 CCDS10626.1 ARFGAP1 CCDS13515.1 ARHGAP10 NM_024605 ARHGAP21 CCDS7144.1 ARHGAP28 NM_001010000 ARHGEF11 CCDS1162.1 ARHGEF7 CCDS9521.1 ARHGEF9 NM_015185 ARID1A CCDS285.1 ARMC7 CCDS11714.1 ARMCX1 CCDS14487.1 ARNT2 NM_014862 ARRDC2 CCDS12370.1 ARSA CCDS14100.1 ARSI NM_001012301 ARTS-1 CCDS4085.1 ASB2 CCDS9915.1 ASXL2 NM_018263 ATF2 CCDS2262.1 ATN1 NM_001940 ATP10A NM_024490 ATP10B ENST00000327245 ATP10D CCDS3476.1 ATP11B NM_014616 ATP1A3 CCDS12594.1 ATP1B2 NM_001678 ATP2A1 CCDS10643.1 ATP2B3 CCDS14722.1 ATP6V0A4 CCDS5849.1 AZU1 CCDS12044.1 B3GALT1 CCDS2227.1 B3GNTL1 NM_001009905 B4GALT7 CCDS4429.1 BACH2 CCDS5026.1 BAI1 NM_001702 BAI3 CCDS4968.1 BAIAP2L2 NM_025045 BAIAP3 CCDS10434.1 BC37295_3 NM_001005850 BCAN CCDS1149.1 BCHE CCDS3198.1 BCL2A1 CCDS10312.1 Beta4GalNAc-T4 CCDS7694.1 BMPR2 NM_001204 BOC CCDS2971.1 BPIL3 CCDS13211.1 BRCA2 CCDS9344.1 BSN CCDS2800.1 BTBD7 NM_001002860 C10orf113 NM_001010896 C10orf31 NM_001012713 C10orf93 CCDS7672.1 C10orf99 CCDS7371.1 C11orf16 CCDS7794.1 C13orf22 CCDS9336.1 C13orf25 CCDS9467.1 C14orf121 NM_138360 C14orf124 NM_020195 C15orf16 CCDS10026.1 C15orf41 NM_032499 C17orf27 NM_020914 C17orf38 NM_001010855 C19orf20 NM_033513 C19orf22 CCDS12048.1 C19orf28 NM_174983 C19orf35 CCDS12087.1 C19orf6 CCDS12052.1 C1orf113 NM_024676 C1orf129 NM_025063 C1orf14 NM_030933 C1orf25 CCDS1366.1 C1orf45 NM_001025231 C1QL2 NM_182528 C1RL CCDS8573.1 C20orf134 NM_001024675 C20orf161 CCDS13377.1 C20orf26 NM_015585 C20orf42 CCDS13098.1 C20orf77 CCDS13301.1 C21orf29 CCDS13712.1 C21orf63 CCDS13614.1 C2orf10 CCDS2291.1 C2orf29 CCDS2050.1 C3 NM_000064 C3orf15 CCDS2994.1 C3orf18 CCDS2829.1 C4orf9 NM_003703 C6orf103 ENST00000326916 C6orf213 NM_001010852 C6orf54 CCDS5304.1 C6orf60 NM_024581 C7orf27 CCDS5334.1 C9orf138 CCDS6487.1 C9orf39 NM_017738 C9orf45 CCDS6850.1 C9orf91 CCDS6808.1 C9orf98 CCDS6954.1 CABLES2 NM_031215 CACNA1A NM_000068 CACNA1E NM_000721 CACNA2D1 CCDS5598.1 CACNG5 CCDS11666.1 CAD CCDS1742.1 CALB1 CCDS6251.1 CALCR CCDS5631.1 CAMSAP1 NM_015447 CAMTA1 NM_015215 CAND2 ENST00000295989 CAPN12 CCDS12519.1 CARD9 CCDS6997.1 CASKIN2 CCDS11723.1 CASP10 CCDS2338.1 CAT CCDS7891.1 CBFA2T2 CCDS13221.1 CBLN4 CCDS13448.1 CCDC11 CCDS11940.1 CCDC18 NM_206886 CCKAR CCDS3438.1 CCL2 CCDS11277.1 CCNB3 CCDS14331.1 CCNYL3 ENST00000332505 CCR1 CCDS2737.1 CCT6A CCDS5523.1 CCT6B NM_006584 CD163 CCDS8578.1 CD1A CCDS1174.1 CD200R1 CCDS2969.1 CD44 CCDS7897.1 CD6 CCDS7999.1 CD79A CCDS12589.1 CD86 CCDS3009.1 CDC42BPA CCDS1558.1 CDH1 CCDS10869.1 CDH10 CCDS3892.1 CDH20 CCDS11977.1 CDH7 CCDS11993.1 CDKN2A CCDS6510.1 CDSN NM_001264 CEBPZ CCDS1787.1 CEECAM1 CCDS6901.1 CEL NM_001807 CELSR1 CCDS14076.1 CENTD1 CCDS3441.1 Cep192 NM_032142 CEP290 NM_025114 CFHR4 NM_006684 CGI-09 CCDS13093.1 CGN CCDS999.1 CHD1 NM_001270 CHD5 CCDS57.1 CHD7 NM_017780 CHI3L1 CCDS1435.1 CHMP1B NM_020412 CHPPR CCDS6182.1 CHST1 CCDS7913.1 CHURC1 NM_145165 CIAS1 CCDS1632.1 CILP CCDS10203.1 CKLFSF4 CCDS10817.1 CLEC4M CCDS12187.1 CLIPR-59 CCDS12486.1 CLK1 CCDS2331.1 CLSTN2 CCDS3112.1 CLUAP1 NM_015041 CMAS CCDS8696.1 CMYA1 CCDS2683.1 CMYA3 NM_152381 CMYA5 NM_153610 CNGB1 NM_001297 CNGB3 CCDS6244.1 CNTN4 CCDS2558.1 CNTN5 NM_014361 CNTN6 CCDS2557.1 CNTNAP2 CCDS5889.1 CNTNAP4 CCDS10924.1 COBLL1 CCDS2223.1 COCH CCDS9640.1 COH1 CCDS6280.1 COL11A1 CCDS778.1 COL14A1 NM_021110 COL17A1 CCDS7554.1 COL22A1 CCDS6376.1 COL4A1 CCDS9511.1 COL4A4 NM_000092 COL5A1 CCDS6982.1 COL6A3 NM_004369 COLEC12 NM_130386 CORO2A CCDS6735.1 CPAMD8 NM_015692 CPLX2 ENST00000274615 CPN1 CCDS7486.1 CPT1C CCDS12779.1 CPZ CCDS3404.1 CREBBP CCDS10509.1 CSF2RB CCDS13936.1 CSMD1 NM_033225 CSMD2 CCDS380.1 CSS3 NM_175856 CTAG2 CCDS14759.1 CTNNA2 NM_004389 CTNNA3 CCDS7269.1 CTNND2 CCDS3881.1 CUBN CCDS7113.1 CUL4B NM_003588 CUTL1 CCDS5720.1 CX40.1 CCDS7191.1 CXorf9 CCDS14614.1 CYFIP1 CCDS10009.1 CYFIP2 NM_014376 CYP1A1 CCDS10268.1 DACH2 CCDS14455.1 DAXX CCDS4776.1 DBT CCDS767.1 DCC1 CCDS6330.1 DCHS1 CCDS7771.1 DCHS2 CCDS3785.1 DCT CCDS9470.1 DDX51 NM_175066 DDX58 CCDS6526.1 DEPDC2 CCDS6201.1 DEPDC5 NM_014662 DET1 NM_017996 DFNB31 CCDS6806.1 DGKA CCDS8896.1 DGKD CCDS2504.1 DGKK NM_001013742 DGKZ CCDS7918.1 DHCR24 CCDS600.1 DHX33 CCDS11072.1 DHX8 CCDS11464.1 DICER1 CCDS9931.1 DIP2B NM_173602 DKFZp313G1735 CCDS4073.1 DKFZP434B0335 NM_015395 DKFZP434G1415 CCDS8743.1 DKFZP434L1717 CCDS3805.1 DKFZp434O0527 CCDS2430.1 DKFZP564J0863 NM_015459 DKFZp566O084 CCDS11215.1 DKFZP586P0123 NM_015531 DKFZp761A052 CCDS14313.1 DLC1 CCDS5989.1 DLEC1 ENST00000337335 DLG2 NM_001364 DLG3 CCDS14403.1 DLGAP1 CCDS11836.1 DMD CCDS14228.1 DMP1 CCDS3623.1 DNA2L ENST00000358410 DNAH11 NM_003777 DNAH5 CCDS3882.1 DNAH8 CCDS4838.1 DNAH9 CCDS11160.1 DNAPTP6 NM_015535 DNHD2 NM_178504 DNM1L CCDS8728.1 DOCK2 CCDS4371.1 DOT1L NM_032482 DP58 NM_001004441 DPP6 NM_130797 DRD2 CCDS8361.1 DRD3 CCDS2978.1 DUOX2 CCDS10117.1 DUSP15 CCDS13193.1 DUSP19 CCDS2289.1 DYSF CCDS1918.1 EBF CCDS4343.1 EBF3 NM_001005463 EDG8 CCDS12240.1 EFEMP1 CCDS1857.1 EHMT1 CCDS7050.1 EIF2AK2 CCDS1786.1 EIF5 CCDS9980.1 EIF5B NM_015904 ELA2 CCDS12045.1 ELAVL4 CCDS553.1 ELN CCDS5562.1 EME2 NM_001010865 EMILIN1 CCDS1733.1 EML1 NM_004434 ENC1 CCDS4021.1 ENST00000294635 ENST00000294635 ENST00000298876 ENST00000298876 ENST00000309390 ENST00000309390 ENST00000322493 ENST00000322493 ENST00000324303 ENST00000324303 ENST00000326382 ENST00000326382 ENST00000326952 ENST00000326952 ENST00000332477 ENST00000332477 ENST00000333971 ENST00000333971 ENST00000334548 ENST00000334548 ENST00000336168 ENST00000336168 ENST00000340260 ENST00000340260 ENST00000356555 ENST00000356555 ENTH NM_014666 EP300 CCDS14010.1 EPB41L1 CCDS13271.1 EPC2 NM_015630 EPHA3 CCDS2922.1 EPHA7 CCDS5031.1 EPHB1 NM_004441 EPHB2 CCDS229.1 EPHB6 CCDS5873.1 EPM2A CCDS5206.1 EPPK1 NM_031308 EPS8L2 NM_022772 ERCC2 NM_000400 ERCC4 NM_005236 ERCC6 CCDS7230.1 EST1B CCDS1137.1 ETS2 CCDS13659.1 ETV6 CCDS8643.1 EVI1 CCDS3205.1 EVPL CCDS11737.1 EXOC2 NM_018303 EXOSC8 NM_181503 F10 CCDS9530.1 F13A1 CCDS4496.1 F8 NM_000132 FAD158 CCDS725.1 FADD CCDS8196.1 FADS1 CCDS8013.1 FADS2 CCDS8012.1 FAM132B ENST00000344233 FAM47B ENST00000329357 FAM50B CCDS4487.1 FAM53B CCDS7641.1 FAM54B NM_019557 FAM55C CCDS2945.1 FAT NM_005245 FAT3 ENST00000298047 FAT4 CCDS3732.1 FBN2 NM_001999 FBN3 CCDS12196.1 FBXO15 CCDS12002.1 FBXO3 CCDS7887.1 FBXO41 ENST00000295133 FBXO9 NM_033481 FBXW7 CCDS3777.1 FBXW8 CCDS9182.1 FGD2 CCDS4829.1 FGD5 NM_152536 FKRP CCDS12691.1 FKSG44 CCDS8102.1 FLJ10324 NM_018059 FLJ10407 CCDS583.1 FLJ10521 CCDS182.1 FLJ10647 CCDS406.1 FLJ12886 NM_019108 FLJ14011 CCDS12944.1 FLJ14299 CCDS6094.1 FLJ14490 CCDS446.1 FLJ14640 NM_032816 FLJ20032 CCDS3666.1 FLJ20035 NM_017631 FLJ20244 CCDS12293.1 FLJ20245 CCDS7041.1 FLJ20457 CCDS6774.1 FLJ20580 CCDS576.1 FLJ21628 CCDS4440.1 FLJ21816 NM_024675 FLJ21986 NM_024913 FLJ23420 CCDS12189.1 FLJ23577 ENST00000303168 FLJ23588 CCDS14049.1 FLJ25006 CCDS11237.1 FLJ25530 CCDS8456.1 FLJ26175 NM_001001668 FLJ31295 CCDS8763.1 FLJ32110 CCDS5613.1 FLJ32112 CCDS587.1 FLJ32416 CCDS12086.1 FLJ32685 CCDS2645.1 FLJ34969 NM_152678 FLJ35220 NM_173627 FLJ35843 CCDS9151.1 FLJ36180 CCDS3851.1 FLJ36748 NM_152406 FLJ37396 CCDS5072.1 FLJ38020 NM_001039775 FLJ38377 CCDS2164.1 FLJ39155 CCDS3924.1 FLJ39501 CCDS12331.1 FLJ39502 CCDS2281.1 FLJ40235 CCDS12827.1 FLJ41046 NM_207479 FLJ41993 NM_001001694 FLJ45231 NM_001039778 FLJ45909 CCDS12522.1 FLJ46072 CCDS6410.1 FLJ46365 CCDS6144.1 FLJ46481 CCDS3384.1 FLJ46536 NM_198483 FLJ90805 CCDS12603.1 FMN2 NM_020066 FMNL1 CCDS11497.1 FMNL3 NM_175736 FMR1 CCDS14682.1 FMR2 CCDS14684.1 FN1 CCDS2399.1 FOXJ1 NM_001454 FOXP2 CCDS5760.1 FREM1 NM_144966 FREM2 NM_207361 FRMPD4 NM_014728 FSTL5 CCDS3802.1 FTCD CCDS13731.1 FTHL17 CCDS14227.1 GABRA1 CCDS4357.1 GABRR1 CCDS5019.1 GALNT13 CCDS2199.1 GALNT4 NM_003774 GALNT8 CCDS8533.1 GAS7 CCDS11152.1 GBP3 CCDS717.1 GDF6 NM_001001557 GFAP CCDS11491.1 GFRA1 CCDS7593.1 GH2 CCDS11648.1 GIMAP7 CCDS5903.1 GJA3 CCDS9289.1 GLB1L3 ENST00000299136 GLI1 CCDS8940.1 GLI3 CCDS5465.1 GLP1R CCDS4839.1 GLTSCR1 NM_015711 GNAT1 CCDS2812.1 GOLGA3 CCDS9281.1 GPC2 CCDS5689.1 GPR CCDS10051.1 GPR110 ENST00000326374 GPR133 CCDS9272.1 GPR151 NM_194251 GPR154 CCDS5443.1 GPR158 NM_020752 GPR35 CCDS2541.1 GPR54 CCDS12049.1 GPR73L1 CCDS13089.1 GPR82 CCDS14259.1 GPRC5C CCDS11699.1 GPS2 CCDS11100.1 GPX6 NM_182701 GRCA CCDS8563.1 GRHL1 NM_198182 GRIA3 CCDS14604.1 GRIK2 CCDS5048.1 GRIN3A CCDS6758.1 GRIP2 ENST00000273083 GRM6 CCDS4442.1 GRM8 CCDS5794.1 GSDML CCDS11354.1 GSR NM_000637 GTF3C1 NM_001520 GTF3C3 CCDS2316.1 GUCA2A CCDS465.1 GUCY1A2 CCDS8335.1 H1T2 CCDS8762.1 HAPLN4 CCDS12398.1 HAS1 CCDS12838.1 HBXIP CCDS824.1 HCK NM_002110 HECW1 CCDS5469.1 HECW2 NM_020760 HELB CCDS8976.1 HELZ NM_014877 HIP1 NM_005338 HIST1H3A CCDS4570.1 HIST1H4I CCDS4620.1 HKR2 CCDS12975.1 HMGCLL1 NM_019036 HOXC10 CCDS8868.1 HOXC9 CCDS8869.1 HOXD4 CCDS2269.1 HPCAL1 CCDS1671.1 HPS5 CCDS7836.1 HRB2 CCDS9012.1 HRPT2 CCDS1382.1 HS3ST2 CCDS10606.1 HS3ST5 NM_153612 HSGT1 CCDS7321.1 HTR1A NM_000524 HYPC CCDS8789.1 IER5 CCDS1343.1 IL12RB1 NM_153701 IL17RB CCDS2874.1 IL17RC CCDS2590.1 IL18R1 CCDS2060.1 IL2RG CCDS14406.1 ILK CCDS7768.1 IMP5 NM_175882 INHBB CCDS2132.1 INO80 CCDS10071.1 INPP5D NM_001017915 INTS2 NM_020748 IQGAP1 CCDS10362.1 IRGQ NM_001007561 IRS4 CCDS14544.1 IRX1 NM_024337 ISYNA1 CCDS12379.1 ITGA11 NM_001004439 ITGA3 CCDS11557.1 ITGA4 NM_000885 ITGA9 CCDS2669.1 ITGAE NM_002208 ITGB4BP CCDS13249.1 ITIH2 NM_002216 ITLN1 CCDS1211.1 ITPR1 NM_002222 IXL NM_017592 JAG1 CCDS13112.1 JM11 CCDS14316.1 JMJD3 ENST00000254846 JPH3 CCDS10962.1 JPH4 CCDS9603.1 K6IRS2 CCDS8833.1 KAL1 CCDS14130.1 KBTBD11 NM_014867 KCNA3 CCDS828.1 KCNA4 NM_002233 KCNB1 CCDS13418.1 KCNB2 CCDS6209.1 KCNC2 CCDS9005.1 KCNC3 CCDS12793.1 KCNJ3 CCDS2200.1 KCNK10 CCDS9880.1 KCNMA1 CCDS7352.1 KCNT1 NM_020822 KCTD15 CCDS12434.1 KEAP1 CCDS12239.1 KIAA0082 CCDS4835.1 KIAA0317 ENST00000338772 KIAA0367 NM_015225 KIAA0372 CCDS4072.1 KIAA0590 CCDS10439.1 KIAA0774 NM_001033602 KIAA1024 NM_015206 KIAA1086 ENST00000262961 KIAA1102 NM_014988 KIAA1109 ENST00000264501 KIAA1219 CCDS13305.1 KIAA1543 ENST00000160298 KIAA1704 CCDS9394.1 KIAA1751 ENST00000270720 KIAA1755 NM_001029864 KIAA1944 CCDS9266.1 KIAA1957 ENST00000332235 KIAA1961 NM_133372 KIAA2013 ENST00000329923 KIF21A NM_017641 KIF25 CCDS5305.1 KIF3A NM_007054 KIN CCDS7080.1 KIRREL CCDS1172.1 KIT CCDS3496.1 KLF5 CCDS9448.1 KLHDC1 CCDS9692.1 KLHDC4 CCDS10963.1 KLP1 CCDS12926.1 KPNB1 CCDS11513.1 KRAS CCDS8702.1 KRT13 CCDS11396.1 KRT9 NM_000226 KRTAP11-1 CCDS13608.1 L3MBTL4 CCDS11839.1 LAMA1 NM_005559 LAMA4 NM_002290 LAMA5 NM_005560 LAMC3 CCDS6938.1 LARP CCDS4328.1 LASS3 CCDS10384.1 LCT CCDS2178.1 LENG8 CCDS12894.1 LGI4 CCDS12444.1 LGR6 CCDS1424.1 LIG3 CCDS11284.1 LIMR CCDS8780.1 LIPH CCDS3272.1 LMOD1 NM_012134 LMTK2 CCDS5654.1 LMX1A CCDS1247.1 LOC113179 CCDS12076.1 LOC113386 NM_138781 LOC123872 CCDS10943.1 LOC126147 NM_145807 LOC128153 CCDS1519.1 LOC130951 NM_138804 LOC131873 ENST00000358511 LOC163131 NM_001005851 LOC167127 CCDS3914.1 LOC222967 ENST00000297186 LOC283219 NM_001029859 LOC283398 ENST00000342823 LOC284434 NM_001007525 LOC339768 CCDS2525.1 LOC340578 NM_001013628 LOC342979 ENST00000340790 LOC343521 NM_001013632 LOC387720 NM_001013633 LOC388135 NM_001039614 LOC392617 ENST00000333066 LOC399706 NM_001010910 LOC441136 NM_001013719 LOC441476 NM_001004353 LOC441722 ENST00000311061 LOC51334 CCDS4127.1 LOC63920 NM_022090 LOC89944 NM_138342 LPAL2 ENST00000342479 LPHN3 NM_015236 LPL CCDS6012.1 LRFN5 CCDS9678.1 LRP1 CCDS8932.1 LRP1B CCDS2182.1 LRP2 CCDS2232.1 LRP3 CCDS12430.1 LRP5 CCDS8181.1 LRRC16 NM_017640 LRRC18 NM_001006939 LRRC3B CCDS2644.1 LRRC4 CCDS5799.1 LRRC48 NM_031294 LRRK2 NM_198578 LRRN3 CCDS5754.1 LRRTM4 NM_024993 MAGEE1 CCDS14433.1 MAMDC1 NM_182830 MAN2A1 NM_002372 MAP1A NM_002373 MAP1B CCDS4012.1 MAP2 CCDS2384.1 MAP2K6 CCDS11686.1 MAP4K2 CCDS8082.1 MAP4K3 CCDS1803.1 MAP4K4 ENST00000302217 MAPKBP1 NM_014994 MAPT CCDS11499.1 MARLIN1 CCDS3385.1 MARS CCDS8942.1 MASP2 CCDS123.1 MASS1 NM_032119 MAST2 NM_015112 MAT2B CCDS4365.1 MBD3 CCDS12072.1 MCM7 CCDS5683.1 MCTP2 NM_018349 MEGF11 CCDS10213.1 MEP1A CCDS4918.1 METTL3 NM_019852 MGC10731 CCDS171.1 MGC13125 CCDS8374.1 MGC15523 CCDS11780.1 MGC15875 CCDS4434.1 MGC20806 CCDS11797.1 MGC2494 CCDS10423.1 MGC26598 CCDS9036.1 MGC26988 CCDS4335.1 MGC29649 CCDS8033.1 MGC33407 CCDS12207.1 MGC34713 CCDS4070.1 MGC35138 CCDS7701.1 MGC35555 CCDS6307.1 MGC39581 CCDS12149.1 MGC4266 CCDS8522.1 MGC50721 CCDS10602.1 MGC5297 CCDS3873.1 MID1 CCDS14138.1 MIZF CCDS8414.1 MKL2 NM_014048 MLC1 CCDS14083.1 MLL NM_005933 MLL2 NM_003482 MLL3 CCDS5931.1 MLL5 NM_182931 MMP9 CCDS13390.1 MOBKL2C CCDS539.1 MORC CCDS2955.1 MORC2 NM_014941 MOXD1 CCDS5152.1 MPHOSPH1 CCDS7407.1 MPL CCDS483.1 MPN2 CCDS1563.1 MPO CCDS11604.1 MPZ CCDS1229.1 MRGPRD ENST00000309106 MRGX1 CCDS7846.1 MRPL38 CCDS11733.1 MRPS7 CCDS11718.1 MSLN NM_013404 MTF1 NM_005955 MTMR12 NM_019061 MTMR2 CCDS8305.1 MTO1 CCDS4979.1 MTR CCDS1614.1 MUC1 CCDS1098.1 MUC15 CCDS7859.1 MUC16 NM_024690 MUC2 NM_002457 MUF1 CCDS533.1 MUM1L1 NM_152423 MYBL1 ENST00000331406 MYBPHL NM_001010985 MYCBPAP NM_032133 MYH2 CCDS11156.1 MYH3 CCDS11157.1 MYH6 CCDS9600.1 MYH9 CCDS13927.1 MYLIP CCDS4536.1 MYO10 NM_012334 MYO15A NM_016239 MYO1G NM_033054 MYO3A CCDS7148.1 MYO6 NM_004999 MYO7B ENST00000272666 MYO9A CCDS10239.1 MYOM1 NM_003803 MYST3 CCDS6124.1 NAALAD2 CCDS8288.1 NAALADL2 NM_207015 NALP10 CCDS7784.1 NALP13 NM_176810 NALP14 CCDS7776.1 NALP4 CCDS12936.1 NAV2 CCDS7850.1 NAV3 NM_014903 NCDN CCDS392.1 NCK1 CCDS3092.1 NCL NM_005381 NCOA2 NM_006540 NEB NM_004543 NEK8 NM_178170 NEO1 CCDS10247.1 NFATC3 CCDS10860.1 NFIA CCDS615.1 NID CCDS1608.1 NID2 CCDS9706.1 NIF3L1BP1 CCDS2900.1 NIPSNAP3B CCDS6761.1 NKX2-2 CCDS13145.1 NLGN1 CCDS3222.1 NMUR1 CCDS2486.1 NOD3 NM_178844 NOL5A CCDS13030.1 NOPE CCDS10206.1 NOR1 CCDS409.1 NOS1 NM_000620 NOX5 NM_024505 NP_001035826.1 ENST00000331090 NP_001074311.1 ENST00000326096 NPD014 CCDS260.1 NPHP4 NM_015102 NPY1R NM_000909 NRG2 CCDS4217.1 NRXN2 CCDS8077.1 NRXN3 CCDS9870.1 NSE1 CCDS1684.1 NTF3 CCDS8538.1 NTRK3 CCDS10340.1 NUDT5 CCDS7089.1 ENST00000318605 ENST00000318605 NUP210 NM_024923 NURIT CCDS9399.1 NXN CCDS10998.1 NXPH3 CCDS11550.1 OBSCN CCDS1570.1 OBSL1 ENST00000265318 OCA2 CCDS10020.1 ODZ4 ENST00000278550 OGDHL CCDS7234.1 OGFOD2 NM_024623 OGT CCDS14414.1 OR10A3 ENST00000360759 OR10K2 NM_001004476 OR10P1 NM_206899 OR10R2 NM_001004472 OR10Z1 NM_001004478 OR11L1 NM_001001959 OR13C3 NM_001001961 OR13C5 NM_001004482 OR1J2 NM_054107 OR2AJ1 ENST00000318244 OR2T1 NM_030904 OR2W3 NM_001001957 OR4A16 NM_001005274 OR4B1 NM_001005470 OR4E2 NM_001001912 OR4L1 NM_001004717 OR4X1 NM_001004726 OR51B4 CCDS7757.1 OR51E1 NM_152430 OR51F2 NM_001004753 OR52I2 NM_001005170 OR52L1 ENST00000332249 OR5C1 NM_001001923 OR5D13 NM_001001967 OR5D3P ENST00000333984 OR5F1 NM_003697 OR5J2 NM_001005492 OR5T1 NM_001004745 OR6A2 CCDS7772.1 OR6K2 NM_001005279 OR8D2 NM_001002918 OR8H1 NM_001005199 OR8K1 NM_001002907 OR8K5 NM_001004058 OR9I1 NM_001005211 OR9K2 NM_001005243 ORC5L CCDS5734.1 OSBPL6 CCDS2277.1 OSCAR CCDS12873.1 OSMR CCDS3928.1 OSTN CCDS3299.1 OTOF CCDS1724.1 OTP CCDS4039.1 OTX1 CCDS1873.1 OVCA2 NM_001383 OVCH1 NM_183378 P11 CCDS8754.1 PABPC5 CCDS14460.1 PACS2 NM_015197 PADI2 CCDS177.1 PALMD CCDS758.1 PAPPA CCDS6813.1 PARP10 NM_032789 PARP14 NM_017554 PARP2 NM_005484 PARP9 CCDS3014.1 PAX6 NM_000280 PB1 CCDS2859.1 PCDH15 CCDS7248.1 PCDH17 NM_014459 PCDH18 NM_019035 PCDH9 CCDS9443.1 PCDHA13 NM_031864 PCDHB16 CCDS4251.1 PCDHB2 CCDS4244.1 PCDHB3 CCDS4245.1 PCDHGA1 NM_031993 PCDHGA11 NM_032091 PCDHGA8 NM_014004 PCDHGC4 CCDS4260.1 PCNT NM_006031 PCNXL2 ENST00000344698 PCSK2 CCDS13125.1 PCSK6 NM_138321 PDE6A CCDS4299.1 PDZRN3 NM_015009 PDZRN4 CCDS8739.1 PEG3 CCDS12948.1 PER3 CCDS89.1 PFAS CCDS11136.1 PGM5 CCDS6622.1 PGR CCDS8310.1 PHACTR3 CCDS13480.1 PHB2 NM_007273 PIAS4 CCDS12118.1 PIGK CCDS674.1 PIGT CCDS13353.1 PIK3CG CCDS5739.1 PIK3R2 CCDS12371.1 PIP5K3 CCDS2382.1 PITRM1 NM_014889 PKD1L2 NM_182740 PKHD1L1 NM_177531 PKIA CCDS6222.1 PKP2 CCDS8731.1 PLCB2 NM_004573 PLCB3 CCDS8064.1 PLCB4 CCDS13104.1 PLEC1 NM_201380 PLEC1 NM_201378 PLEK2 CCDS9782.1 PLEKHA6 CCDS1444.1 PLEKHG2 NM_022835 PLK5_HUMAN ENST00000334770 PLXNA1 NM_032242 PLXNB1 CCDS2765.1 PMP22CD NM_001013743 PNPLA1 NM_001039725 PODN CCDS573.1 PODXL NM_001018111 POLR2A NM_000937 POLRMT CCDS12036.1 PON1 CCDS5638.1 PPA2 CCDS3667.1 PPFIA2 NM_003625 PPP1CA CCDS8160.1 PPP1R15B CCDS1445.1 PPP1R3A CCDS5759.1 PPP2R1A CCDS12849.1 PPP2R3A CCDS3087.1 PPP2R4 CCDS6920.1 PPP5C CCDS12684.1 PRDM10 CCDS8484.1 PRDM5 CCDS3716.1 PRDM9 NM_020227 PRELP CCDS1438.1 PREX1 CCDS13410.1 PRG-3 CCDS6751.1 PRKACG CCDS6625.1 PRKCG CCDS12867.1 PRKD1 CCDS9637.1 ProSAPiP1 CCDS13049.1 PRR12 ENST00000246798 PRSS23 CCDS8278.1 PSMD3 CCDS11356.1 PSME4 NM_014614 PTCHD2 ENST00000294484 PTCHD3 NM_001034842 PTF1A CCDS7143.1 PTGER3 CCDS652.1 PTN CCDS5844.1 PTPN12 CCDS5592.1 PTPRK CCDS5137.1 PTPRZ1 NM_002851 PUM1 CCDS338.1 PWP2H NM_005049 PXDN ENST00000252804 PXDNL NM_144651 PYHIN1 CCDS1178.1 Q08AG5_HUMAN ENST00000334213 Q5JX50_HUMAN ENST00000325076 Q5SYT8_HUMAN ENST00000279434 Q6ZMX6_HUMAN ENST00000269197 Q6ZT40_HUMAN ENST00000296564 Q7Z2Q7_HUMAN ENST00000334994 Q7Z7L8_HUMAN ENST00000339446 Q8N2V9_HUMAN ENST00000324414 Q8N5S4_HUMAN ENST00000326474 Q8N6V7_HUMAN ENST00000324928 Q8N800_HUMAN ENST00000322516 Q8N9F6_HUMAN ENST00000317122 Q8N9G5_HUMAN ENST00000313957 Q8N9S5_HUMAN ENST00000329388 Q8N9V7_HUMAN ENST00000309765 Q8N9Z1_HUMAN ENST00000326413 Q8NCK2_HUMAN ENST00000325720 Q8NGP7_HUMAN ENST00000341231 Q8NH06_HUMAN ENST00000324144 Q8NH08_HUMAN ENST00000327198 Q96GK3_HUMAN ENST00000315264 Q96M18_HUMAN ENST00000335239 Q96MJ2_HUMAN ENST00000327832 Q96QE0_HUMAN ENST00000301647 Q96RX8_HUMAN ENST00000301719 Q96S27_HUMAN ENST00000301682 Q9H557_HUMAN ENST00000237253 Q9H5F0_HUMAN ENST00000360484 Q9H8A7_HUMAN ENST00000053084 Q9HA39_HUMAN ENST00000329980 Q9HCM3_HUMAN ENST00000242365 Q9NSI0_HUMAN ENST00000328881 Q9NT86_HUMAN ENST00000314272 Q9P169_HUMAN ENST00000342338 Q9P193_HUMAN ENST00000359406 Q9P1M5_HUMAN ENST00000303007 Q9Y6V0-3 ENST00000333891 QRICH2 NM_032134 RAB6B CCDS3082.1 RAD9B CCDS9148.1 RAG1 CCDS7902.1 RAG2 CCDS7903.1 RaLP CCDS10130.1 RANBP2 CCDS2079.1 RARB CCDS2642.1 RARRES2 CCDS5902.1 RASEF ENST00000330861 RASGRP3 NM_170672 RASGRP4 NM_170603 RASIP1 CCDS12731.1 RASSF6 CCDS3558.1 RBAF600 CCDS189.1 RBBP6 CCDS10621.1 RBM27 ENST00000265271 RC74 NM_018250 RCHY1 CCDS3567.1 RDH8 CCDS12223.1 RELN NM_005045 RENBP CCDS14738.1 REPIN1 NM_013400 RFX1 CCDS12301.1 RFX3 CCDS6449.1 RFXDC1 CCDS5113.1 RGS11 CCDS10403.1 RGS17 CCDS5244.1 RHBDF1 NM_022450 RHOT2 CCDS10417.1 RIC3 CCDS7788.1 RIMBP2 NM_015347 RIMS1 NM_014989 RIMS2 NM_014677 RLF CCDS448.1 RNF175 NM_173662 RNUT1 CCDS10281.1 RODH CCDS8925.1 RP1 CCDS6160.1 RPGRIP1 NM_020366 RREB1 NM_001003699 RTL1 ENST00000331067 RTTN NM_173630 RUNX1T1 CCDS6256.1 RYR1 NM_000540 RYR2 NM_001035 SACS CCDS9300.1 SARS2 NM_017827 SART3 CCDS9117.1 SBLF CCDS1840.1 SCAP2 CCDS5400.1 SCFD2 NM_152540 SCGN CCDS4561.1 SCN11A NM_014139 SCN2A2 NM_021007 SCN4A NM_000334 SCN5A NM_000335 SCN5A NM_198056 SCN7A NM_002976 SCNM1 CCDS987.1 SCNN1B CCDS10609.1 SCNN1G CCDS10608.1 SCRIB CCDS6411.1 SDPR CCDS2313.1 SDS CCDS9169.1 SEC14L3 CCDS13877.1 SEMA4D CCDS6685.1 SEMA5B CCDS3019.1 SENP1 NM_014554 SESN2 CCDS321.1 SEZ6L CCDS13833.1 SF3A1 CCDS13875.1 SF3B1 NM_012433 SFRS12 CCDS3991.1 SFRS16 CCDS12652.1 SGEF NM_015595 SH2D1B NM_053282 SH3GL3 CCDS10325.1 SH3TC1 CCDS3399.1 SHANK2 CCDS8198.1 SHKBP1 CCDS12560.1 SI CCDS3196.1 SIDT1 CCDS2974.1 SIGLEC11 CCDS12790.1 SIPA1L2 NM_020808 SIX2 CCDS1822.1 SKD3 CCDS8215.1 SLC14A1 CCDS11925.1 SLC17A1 CCDS4565.1 SLC17A7 CCDS12764.1 SLC1A6 CCDS12321.1 SLC22A15 NM_018420 SLC22A7 CCDS4893.1 SLC25A26 CCDS2905.1 SLC28A3 CCDS6670.1 SLC2A1 CCDS477.1 SLC2A3 CCDS8586.1 SLC2A5 CCDS99.1 SLC33A1 CCDS3173.1 SLC39A10 NM_020342 SLC39A6 NM_012319 SLC45A1 ENST00000289877 SLC4A10 NM_022058 SLC4A8 CCDS8814.1 SLC4A9 NM_031467 SLC6A15 CCDS9026.1 SLC6A17 NM_001010898 SLC6A2 CCDS10754.1 SLC6A3 CCDS3863.1 SLC9A5 NM_004594 SLCO1A2 CCDS8686.1 SLCO1B1 CCDS8685.1 SLCO1C1 CCDS8683.1 SLCO4C1 NM_180991 SLITRK2 CCDS14680.1 SLITRK3 CCDS3197.1 SLITRK5 CCDS9465.1 SMAD3 CCDS10222.1 SMAD4 CCDS11950.1 SMARCA4 CCDS12253.1 SMOC1 CCDS9798.1 SMTN CCDS13886.1 SN CCDS13060.1 SNCAIP CCDS4131.1 SNRPC NM_003093 SNX16 CCDS6234.1 SNX26 CCDS12477.1 SORL1 CCDS8436.1 SOX3 CCDS14669.1 SP8 CCDS5372.1 SPAP1 CCDS1168.1 SPATA13 ENST00000360220 SPINLW1 CCDS13359.1 SPTAN1 CCDS6905.1 SPTBN2 CCDS8150.1 SR140_HUMAN ENST00000319822 SRCRB4D CCDS5585.1 SRRM2 NM_016333 SST CCDS3288.1 ST6GAL2 CCDS2073.1 ST6GALNAC5 CCDS673.1 ST8SIA5 CCDS11930.1 STAB1 NM_015136 STAC CCDS2662.1 STAC2 CCDS11335.1 STAMBP CCDS1929.1 STARD13 CCDS9348.1 STARD8 CCDS14390.1 STAT4 CCDS2310.1 STIM1 CCDS7749.1 STK10 NM_005990 STK23 NM_014370 STK33 CCDS7789.1 STMN4 CCDS6055.1 STN2 CCDS9875.1 SULF1 CCDS6204.1 SULF2 CCDS13408.1 SV2A CCDS940.1 SYNE1 CCDS5236.1 SYNE1 CCDS5237.1 SYNE2 CCDS9761.1 SYP CCDS14321.1 SYT1 CCDS9017.1 SYT6 CCDS871.1 SYT7 NM_004200 T CCDS5290.1 TAF1B NM_005680 TAF1L NM_153809 TAF4 NM_003185 TAS2R41 NM_176883 TATDN2 NM_014760 TBC1D14 CCDS3394.1 TBX15 NM_152380 TBX18 ENST00000330469 TBX5 CCDS9173.1 TBX6 CCDS10670.1 TCEB3B CCDS11932.1 TCFL1 CCDS989.1 TDRD7 CCDS6725.1 TENC1 CCDS8842.1 TESSP2 NM_182702 TEX14 NM_198393 TFCP2L1 CCDS2134.1 TFF2 CCDS13684.1 TFPI2 CCDS5632.1 TFR2 NM_003227 TFSM1_HUMAN ENST00000314720 TG NM_003235 TGFBR2 CCDS2648.1 TGIF2 CCDS13278.1 THNSL1 CCDS7147.1 THSD7B ENST00000272643 TIMELESS CCDS8918.1 TJP1 NM_175610 TLL2 CCDS7449.1 TM7SF4 CCDS6301.1 TM9SF4 CCDS13196.1 TMCC2 NM_014858 TMEFF2 CCDS2314.1 TMEM132B NM_052907 TMEM16A NM_018043 TMEM16C NM_031418 TMEM16G NM_001001891 TMEM63B NM_018426 TMEM8 CCDS10407.1 TMEPAI CCDS13462.1 TMPO CCDS9064.1 TMPRSS13 NM_032046 TNF CCDS4702.1 TNFRSF8 CCDS144.1 TNK1 NM_003985 TNNI3 NM_000363 TNR CCDS1318.1 TOR3A CCDS1329.1 TP53 CCDS11118.1 TP53BP1 CCDS10096.1 TPO CCDS1642.1 TREH NM_007180 TRERF1 CCDS4867.1 TRIM37 NM_001005207 TRIM58 CCDS1636.1 TRPM1 CCDS10024.1 TRPM2 CCDS13710.1 TRPM3 CCDS6634.1 TSC2 CCDS10458.1 TSP-NY CCDS9237.1 TSTA3 CCDS6408.1 TTBK2 NM_173500 TTC12 CCDS8360.1 TTC21B NM_024753 TTC24 ENST00000340086 TTF1 CCDS6948.1 TTK CCDS4993.1 TTN NM_133378 TTN NM_133437 TUBB3 CCDS10988.1 TXNDC6 CCDS3099.1 UBE1L CCDS2805.1 UBE2M CCDS12987.1 UBQLN4 CCDS1127.1 UBR2 CCDS4870.1 UBXD7 ENST00000296328 UCP3 CCDS8229.1 ULBP1 CCDS5223.1 UNC13C ENST00000260323 USP20 NM_001008563 USP31 CCDS10607.1 USP38 CCDS3758.1 USP42 NM_032172 UTRN NM_007124 VDAC2 CCDS7348.1 VGCNL1 CCDS9498.1 VIM CCDS7120.1 VIT NM_053276 VLDLR CCDS6446.1 VMD2L1 NM_017682 VPS13A CCDS6655.1 VPS13D NM_018156 VPS16 CCDS13036.1 VPS39 CCDS10083.1 VSIG1 CCDS14535.1 VWF CCDS8539.1 WASF3 CCDS9318.1 WBSCR14 CCDS5553.1 WBSCR17 CCDS5540.1 WDR1 NM_005112 WDR17 CCDS3825.1 WDR27 NM_182552 WDR42B ENST00000329763 WDR44 CCDS14572.1 WHSC1 CCDS3357.1 WIRE CCDS11364.1 WNT9A NM_003395 WRNIP1 CCDS4475.1 XKR4 NM_052898 XPNPEP1 CCDS7560.1 XPO7 NM_015024 XR_017918.1 ENST00000258651 XYLT2 CCDS11563.1 YLPM1 ENST00000238571 YN002_HUMAN ENST00000334389 ZAN NM_173059 ZBTB24 NM_014797 ZBTB33 CCDS14596.1 ZBTB7 CCDS12119.1 ZC3H12B NM_001010888 ZC3HDC7 CCDS10550.1 ZDHHC4 CCDS5352.1 ZFHX1B CCDS2186.1 ZFP36 CCDS12534.1 ZHX3 CCDS13315.1 ZIM3 NM_052882 ZMAT4 NM_024645 ZNF133 CCDS13134.1 ZNF136 NM_003437 ZNF148 CCDS3031.1 ZNF238 CCDS1623.1 ZNF253 ENST00000327867 ZNF31 NM_145238 ZNF333 CCDS12316.1 ZNF334 NM_199441 ZNF365 CCDS7264.1 ZNF423 NM_015069 ZNF443 NM_005815 ZNF451 CCDS4960.1 ZNF507 NM_014910 ZNF537 CCDS12421.1 ZNF560 CCDS12214.1 ZNF614 CCDS12847.1 ZNF638 CCDS1917.1 ZNF645 CCDS14205.1 ZNF648 ENST00000339948 ZNF682 NM_033196 ZYG11B NM_024646 Note: Gene symbols are standard symbols assigned by Entrz Gene (http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene). Accession IDs “NM_XXXX” are uniquely assigned to each gene by National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/sites/entrez?db=nuccore). Accession IDs “CCDSXXXX” are uniquely assigned to individual genes by National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/CCDS/). Accession IDs “ENSTXXXXXXXXXXX” are uniquely assigned to individual genes by Ensembl (http://www.ensembl.org/index.html).

TABLE 14 Genes containing somatic mutations in breast cancer adapted from the paper by Wood et. al. (Wood et al., 2007). Gene Symbol Accession ID ABCA12 NM_173076 ABCA3 NM_001089.1 ABCA4 NM_000350.1 ABCB10 NM_012089.1 ABCB6 NM_005689.1 ABCB8 NM_007188.2 ABL2 NM_007314 ABLIM1 NM_002313.4 ABP1 NM_001091 ACADM NM_000016.2 ACO2 NM_001098.2 ACY1 NM_000666.1 ADAM12 NM_003474.2 ADAMTS16 NM_139056 ADAMTS19 NM_133638.1 ADAR NM_001111.2 ADH1B NM_000668 ADHFE1 NM_144650.1 ADRA1A NM_033302.1 AEGP NM_206920.1 AGBL4 NM_032785 AGC1 NM_001135 AGRN NM_198576 AHRR NM_020731 AHSA2 NM_152392.1 AIM1 NM_001624 AKAP6 NM_004274.3 AKAP8 NM_005858.2 AKAP9 NM_005751.3 ALCAM NM_001627 ALMS1 NM_015120 ALS2 NM_020919 ALS2CL NM_147129.2 ALS2CR12 NM_139163.1 ALS2CR19 NM_152526 AMFR NM_001144.3 AMIGO1 NM_020703 AMOTL1 NM_130847 AMPD2 NM_139156.1 AMPD2 NM_004037.5 ANAPC5 NM_016237.3 ANK1 NM_020476.1 ANK2 NM_001148.2 ANKRD28 NM_015199 ANKRD29 NM_173505.1 ANKRD30A NM_052997.1 ANKRD5 NM_198798.1 AP1M1 NM_032493.2 AP3B2 NM_004644 APBB1 NM_145689 APC2 NM_005883.1 APCS NM_001639.2 APOC4 NM_001646.1 APOL1 NM_145343.1 APPL NM_012096.1 APXL NM_001649.2 AQP8 NM_001169.2 ARC NM_015193 ARFGAP3 NM_014570.3 ARFGEF2 NM_006420.1 ARFRP1 NM_003224.2 ARHGAP11A NM_014783.2 ARHGAP25 NM_001007231 ARHGEF4 NM_015320.2 ARID1B NM_017519.1 ARRB1 NM_020251 ARRDC3 NM_020801 ARV1 NM_022786.1 ASB11 NM_080873.1 ASGR1 NM_001671.2 ASL NM_000048.2 ASTN2 NM_014010.3 ATCAY NM_033064 ATF2 NM_001880.2 ATN1 NM_001940 ATP10A NM_024490 ATP12A NM_001676 ATP2A3 NM_174955.1 ATP6AP1 NM_001183 ATP6V0B NM_004047.2 ATP8B1 NM_005603.1 ATP8B4 NM_024837 ATRN NM_139321.1 ATXN2 NM_002973 AVPI1 NM_021732.1 AVPR2 NM_000054.2 B3GALNT2 NM_152490.1 B3GALT4 NM_003782 BAI1 NM_001702 BAP1 NM_004656.2 BAT2 NM_080686.1 BAT3 NM_080703.1 BAZ1A NM_013448.2 BAZ1B NM_032408.1 BC002942 NM_033200.1 BCAR1 NM_014567.2 BCCIP NM_016567.2 BCL11A NM_018014.2 BCORL1 NM_021946.2 BGN NM_001711.3 BLR1 NM_001716.2 BMP1 NM_006129.2 BOC NM_033254.2 BRCA1 NM_007296.1 BRCA2 NM_000059.1 BSPRY NM_017688 C10orf30 NM_152751.1 C10orf38 NM_001010924 C10orf39 NM_194303.1 C10orf45 NM_031453.2 C10orf54 NM_022153 C10orf56 NM_153367.1 C10orf64 NM_173524 C11orf37 NM_001007543 C11orf9 NM_013279 C13orf24 NM_006346 C14orf100 NM_016475 C14orf101 NM_017799.2 C14orf121 NM_138360 C14orf155 NM_032135.2 C14orf161 NM_024764 C14orf21 NM_174913.1 C14orf29 NM_181814.1 C14orf46 NM_001024674 C17orf47 NM_001038704 C17orf64 NM_181707 C18orf19 NM_152352.1 C19orf28 NM_174983 C19orf6 NM_033420.2 C1orf190 NM_001013615 C1orf2 NM_006589.2 C1QB NM_000491.2 C20orf103 NM_012261.2 C20orf121 NM_024331.2 C20orf161 NM_033421.2 C20orf177 NM_022106.1 C20orf23 NM_024704.3 C20orf44 NM_018244.3 C22orf19 NM_003678.3 C4orf14 NM_032313.2 C5orf14 NM_024715.2 C6orf102 NM_145027.3 C6orf145 NM_183373.2 C6orf174 NM_001012279 C6orf204 NM_206921.1 C6orf21 NM_001003693 C6orf213 NM_001010852 C6orf31 NM_030651.2 C7orf11 NM_138701.1 C9orf126 NM_173690 C9orf37 NM_032937 C9orf67 NM_032728.2 CACNA1B NM_000718 CACNA1F NM_005183 CACNA1G NM_198385 CACNA1H NM_021098 CACNA1I NM_001003406 CACNA2D3 NM_018398 CAMTA1 NM_015215 CAPN11 NM_007058 CBFB NM_001755.2 CCDC16 NM_052857 CCDC18 NM_206886 CCDC66 NM_001012506 CD2 NM_001767.2 CD74 NM_001025159 CD97 NM_001784 CDC27 NM_001256.2 CDH10 NM_006727.2 CDH20 NM_031891.2 CDH8 NM_001796.2 CDKL2 NM_003948.2 CDON NM_016952.2 CDS1 NM_001263.2 CENPE NM_001813 CENTB1 NM_014716.2 CENTD3 NM_022481.4 CENTG1 NM_014770.2 CEP290 NM_025114 CFHL5 NM_030787.1 CFL2 NM_138638.1 CGI-14 NM_015944.2 CGI-37 NM_016101.2 CHD1 NM_001270 CHD5 NM_015557.1 CHD7 NM_017780 CHD8 NM_020920 CHD9 NM_025134 CHRND NM_000751.1 CIC NM_015125.2 CLCA2 NM_006536.3 CLCN1 NM_000083.1 CLCN3 NM_001829 CLEC6A NM_001007033 CLSPN NM_022111.2 CLUAP1 NM_015041 CMYA1 NM_194293.2 CMYA4 NM_173167.1 CNGA2 NM_005140.1 CNGB1 NM_001297 CNNM4 NM_020184.2 CNTN3 NM_020872 CNTN5 NM_014361 CNTN6 NM_014461.2 COG3 NM_031431.2 COH1 NM_017890.3 COL11A1 NM_001854.2 COL12A1 NM_004370 COL19A1 NM_001858.3 COL4A4 NM_000092 COL7A1 NM_000094.2 COMMD7 NM_053041 COPG NM_016128 COQ9 NM_020312 CPA3 NM_001870.1 CPAMD8 NM_015692 CPEB1 NM_030594 CPS1 NM_001875.2 CPSF3 NM_016207.2 CROCC NM_014675 CRR9 NM_030782.2 CRSP2 NM_004229.2 CRTC1 NM_025021 CRX NM_000554.2 CRYAA NM_000394.2 CSEN NM_013434.3 CSMD1 NM_033225 CSMD3 NM_198123.1 CSNK1D NM_001893.3 CSPP1 NM_024790 CST4 NM_001899.2 CTF8 NM_001039690 CTNNA1 NM_001903 CTNNA2 NM_004389 CTNND1 NM_001331 CUBN NM_001081.2 CUTC NM_015960.1 CUTL1 NM_001913.2 CUTL2 NM_015267 CYP1A1 NM_000499.2 CYP1A2 NM_000761 CYP26A1 NM_000783.2 CYP2D6 NM_000106 CYP4A22 NM_001010969 DACH1 NM_080759 DAZAP1 NM_018959.2 DBN1 NM_004395.2 DC2 NM_021227.2 DDO NM_003649.2 DDX10 NM_004398.2 DDX18 NM_006773.3 DDX3X NM_024005.1 DEFB128 NM_001037732 DENND2A NM_015689 DGKB NM_004080 DGKE NM_003647.1 DGKG NM_001346.1 DHX32 NM_018180.2 DIP NM_015124 DIP2B NM_173602 DKFZP564B1023 NM_031306.1 DKFZP564J102 NM_001006655 DKFZp761I2123 NM_031449 DKFZp779B1540 NM_001010903 DKK3 NM_015881.4 DLEC1 NM_007335.1 DMD NM_004006.1 DNAH17 NM_003727 DNAH5 NM_001369.1 DNAH9 NM_001372.2 DNAJA3 NM_005147.3 DNAJA5 NM_194283.1 DNAJC10 NM_018981 DNAJC13 NM_015268 DNASE1L3 NM_004944.1 DNM2 NM_004945 DNM3 NM_015569 DOCK1 NM_001380 DPAGT1 NM_001382.2 DPAGT1 NM_203316.1 DPP10 NM_020868 DPP6 NM_130797 DPYD NM_000110 DRIM NM_014503.1 DSCR6 NM_018962.1 DSG2 NM_001943 DTNA NM_032978.4 DTX3L NM_138287.2 DUOX1 NM_017434 DVL3 NM_004423.3 DYSF NM_003494.2 ECT2 NM_018098.4 EDEM1 NM_014674 EDNRA NM_001957.1 EEF1G NM_001404 EGFL6 NM_015507.2 EHBP1 NM_015252.2 EHMT1 NM_024757.3 EIF4A2 NM_001967.2 EIF4B NM_001417 EIF5 NM_183004.3 ELA1 NM_001971.3 ELAVL3 NM_001420 ENPEP NM_001977.2 EOMES NM_005442.2 EP400 NM_015409 EPC2 NM_015630 ERCC3 NM_000122.1 ERCC6 NM_000124.1 EREG NM_001432.1 ETV5 NM_004454 EVI2A NM_001003927 EVI5 NM_005665 EXOC2 NM_018303 EXOC5 NM_006544 EXOSC3 NM_016042 FAAH NM_001441.1 FABP4 NM_001442.1 FAM44A NM_148894.1 FAM47B NM_152631.1 FAM80B NM_020734 FANCA NM_000135 FANCM NM_020937 FARP1 NM_005766.1 FBXO40 NM_016298 FBXO8 NM_012180.1 FBXW11 NM_012300 FCHO1 NM_015122 FCMD NM_006731.1 FCRH3 NM_052939.2 FEM1C NM_020177.2 FER1L3 NM_133337 FGD3 NM_033086 FGD6 NM_018351 FGFR2 NM_022970.1 FHOD1 NM_013241.1 FHOD3 NM_025135 FLG2 NM_001014342 FLJ10241 NM_018035 FLJ10292 NM_018048.2 FLJ10324 NM_018059 FLJ10458 NM_018096.2 FLJ10726 NM_018195.2 FLJ10874 NM_018252.1 FLJ13089 NM_024953.2 FLJ13231 NM_023073 FLJ13479 NM_024706.3 FLJ13868 NM_022744.1 FLJ14503 NM_152780.2 FLJ14624 NM_032813.1 FLJ16331 NM_001004326 FLJ20152 NM_019000 FLJ20184 NM_017700.1 FLJ20422 NM_017814.1 FLJ20584 NM_017891.2 FLJ20604 NM_017897.1 FLJ21839 NM_021831.3 FLJ21945 NM_025203.1 FLJ23584 NM_024588 FLJ25955 NM_178821.1 FLJ31413 NM_152557.3 FLJ32115 NM_152321.1 FLJ32363 NM_198566.1 FLJ32440 NM_173685.1 FLJ32830 NM_152781.1 FLJ34521 NM_001039787 FLJ36180 NM_178556.3 FLJ36748 NM_152406 FLJ40342 NM_152347.3 FLJ40869 NM_182625.2 FLJ41821 NM_001001697 FLJ45455 NM_207386 FLJ46321 NM_001001670 FLJ46354 NM_198547.1 FLJ46481 NM_207405.1 FLJ90579 NM_173591.1 FLNA NM_001456 FLNB NM_001457.1 FLNC NM_001458 FMNL3 NM_175736 FMOD NM_002023 FN1 NM_002026.2 FNDC3B NM_022763.2 FOLR2 NM_000803.2 FOXP2 NM_014491.1 FOXP4 NM_138457.1 FREM1 NM_144966 FRMPD1 NM_014907.1 FUCA1 NM_000147.2 FUS NM_004960.1 FXR1 NM_005087.1 G3BP2 NM_203505.1 G6PC NM_000151.1 GA17 NM_006360.2 GAB1 NM_002039.2 GABRA4 NM_000809.2 GABRP NM_014211.1 GALK2 NM_001001556 GALNT17 NM_001034845 GALNT5 NM_014568.1 GALNTL2 NM_054110 GARNL1 NM_194301 GDF6 NM_001001557 GGA1 NM_013365.2 GGA3 NM_014001.2 GIMAP1 NM_130759.2 GIMAP8 NM_175571 GIOT-1 NM_153257 GIPC3 NM_133261 GJA8 NM_005267 GJB1 NM_000166.2 GKN1 NM_019617.2 GLG1 NM_012201 GLI1 NM_005269.1 GLT25D2 NM_015101.1 GMCL1L NM_022471.2 GNB1L NM_053004.1 GNPAT NM_014236.1 GOLGA7 NM_016099 GOLGB1 NM_004487.1 GOLPH4 NM_014498.2 GORASP2 NM_015530 GP5 NM_004488.1 GPC1 NM_002081.1 GPC2 NM_152742.1 GPHB5 NM_145171 GPNMB NM_002510.1 GPR115 NM_153838.1 GPR45 NM_007227.3 GPR7 NM_005285.1 GPR81 NM_032554.2 GRIK2 NM_021956.2 GRIK3 NM_000831.2 GRIN2C NM_000835 GRIN2D NM_000836.1 GRIPAP1 NM_207672 GRM6 NM_000843.2 GSDML NM_018530.1 GSN NM_000177.3 GTF2A1 NM_015859.2 GTF3C1 NM_001520 GUCY2F NM_001522.1 HADHB NM_000183.1 HCN3 NM_020897.1 HDAC4 NM_006037.2 HDAC7A NM_015401.1 HDLBP NM_203346.1 HEBP1 NM_015987 HEL308 NM_133636.1 HIST1H4L NM_003546.2 HIST2H2AB NM_175065.2 HK3 NM_002115.1 HLCS NM_000411.4 HM13 NM_030789.2 HMG2L1 NM_001003681 HOMER2 NM_199331 HOOK1 NM_015888.3 HOOK2 NM_013312 HOOK3 NM_032410.2 HOXA3 NM_153631.1 HOXA4 NM_002141.2 HS3ST4 NM_006040 HSD11B1 NM_181755.1 HSD17B8 NM_014234.3 HSHIN1 NM_199324.1 HSPA14 NM_016299.1 HSPA1B NM_005346 HSPC049 NM_014149 HTF9C NM_182984.2 HUMCYT2A NM_015848.1 HUWE1 NM_031407 ICAM5 NM_003259.2 IFNA2 NM_000605.2 IFNB1 NM_002176.1 IKBKAP NM_003640.2 IKBKB NM_001556.1 IL1RAPL2 NM_017416.1 IL7R NM_002185.2 INA NM_032727.2 INHBE NM_031479.3 IPLA2(GAMMA) NM_015723 IPO7 NM_006391 IQSEC2 NM_015075 IRF8 NM_002163.1 IRS4 NM_003604.1 IRTA2 NM_031281.1 ITGA9 NM_002207.1 ITGAE NM_002208 ITGAL NM_002209 ITGB2 NM_000211.1 ITPR1 NM_002222 ITR NM_180989.3 JARID1B NM_006618 JMJD1A NM_018433.3 JMJD1C NM_004241 JUP NM_021991.1 KCNA5 NM_002234.2 KCNC2 NM_139136.2 KCNJ1 NM_000220.2 KCNJ15 NM_170737.1 KCNQ3 NM_004519 KEAP1 NM_203500.1 KIAA0100 NM_014680 KIAA0143 NM_015137 KIAA0256 NM_014701 KIAA0284 NM_015005 KIAA0367 NM_015225 KIAA0427 NM_014772.1 KIAA0467 NM_015284 KIAA0513 NM_014732 KIAA0528 NM_014802 KIAA0664 NM_015229 KIAA0672 NM_014859 KIAA0676 NM_015043.3 KIAA0703 NM_014861 KIAA0774 NM_001033602 KIAA0789 NM_014653 KIAA0863 NM_014913 KIAA0913 NM_015037 KIAA0934 NM_014974.1 KIAA0999 NM_025164.3 KIAA1012 NM_014939.2 KIAA1117 NM_015018.2 KIAA1161 NM_020702 KIAA1324 NM_020775.2 KIAA1377 NM_020802 KIAA1414 NM_019024 KIAA1632 NM_020964.1 KIAA1797 NM_017794 KIAA1826 NM_032424 KIAA1914 NM_001001936 KIAA1946 NM_177454 KIBRA NM_015238.1 KIF14 NM_014875 KIR2DS4 NM_012314.2 KLHL10 NM_152467 KLHL15 NM_030624 KLK15 NM_017509.2 KPNA5 NM_002269.2 KRTAP10-8 NM_198695.1 KRTAP20-1 NM_181615.1 KTN1 NM_182926.1 LAMA1 NM_005559 LAMA2 NM_000426.2 LAMA4 NM_002290 LAMB4 NM_007356 LAP1B NM_015602.2 LDHB NM_002300.3 LEPREL1 NM_018192.2 LGALS2 NM_006498.1 LHCGR NM_000233.1 LIP8 NM_053051.1 LIPE NM_005357.2 LLGL1 NM_004140 LMO6 NM_006150.3 LOC112703 NM_138411 LOC113179 NM_138422.1 LOC113828 NM_138435.1 LOC123876 NM_001010845 LOC126248 NM_173479.2 LOC200420 NM_145300 LOC220929 NM_182755.1 LOC253012 NM_198151.1 LOC255374 NM_203397 LOC283849 NM_178516.2 LOC339123 NM_001005920 LOC339745 NM_001001664 LOC340156 NM_001012418 LOC374955 NM_198546.1 LOC388595 NM_001013641 LOC388915 NM_001010902 LOC389151 NM_001013650 LOC389549 NM_001024613 LOC440925 NM_001013712 LOC440944 NM_001013713 LOC441070 NM_001013715 LOC646870 NM_001039790 LOC652968 NM_001037666 LOC88523 NM_033111 LOC90529 NM_178122.2 LOC91461 NM_138370 LOXL2 NM_002318 LPO NM_006151 LRBA NM_006726.1 LRRC16 NM_017640 LRRC4 NM_022143.3 LRRC43 NM_152759 LRRC7 NM_020794.1 LRRFIP1 NM_004735.1 LUZP5 NM_017760 LYST NM_000081 LYST NM_001005736 LZTS2 NM_032429.1 MACF1 NM_012090.3 MAGEA1 NM_004988.3 MAGEA4 NM_002362.3 MAGEB10 NM_182506 MAGEC2 NM_016249.2 MAGED2 NM_201222.1 MAGEE1 NM_020932.1 MAGI1 NM_173515.1 MANEA NM_024641.2 MAOA NM_000240.2 MAP1A NM_002373 MAP3K6 NM_004672.3 MAPK13 NM_002754.3 MAPKBP1 NM_014994 MASP1 NM_001879 MAZ NM_002383 MCAM NM_006500 MCART1 NM_033412.1 MCF2L2 NM_015078.2 MCOLN1 NM_020533.1 MDC1 NM_014641 MED12 NM_005120 MEF2C NM_002397 MFAP5 NM_003480.2 MGC11332 NM_032718.2 MGC17299 NM_144626.1 MGC21688 NM_144635.3 MGC24047 NM_178840.2 MGC27019 NM_144705.2 MGC33212 NM_152773 MGC33370 NM_173807.2 MGC33657 NM_001029996 MGC34837 NM_152377.1 MGC42174 NM_152383 MGC5297 NM_024091.2 MIA2 NM_054024.3 MICAL1 NM_022765.2 MICAL-L1 NM_033386.1 MKLN1 NM_013255 MLL4 NM_014727 MLLT2 NM_005935.1 MMP10 NM_002425.1 MMP15 NM_002428.2 MOGAT1 NM_058165 MOSPD1 NM_019556.1 MPFL NM_001025190 MRE11A NM_005590.2 MSI1 NM_002442.2 MTA1 NM_004689 MTAC2D1 NM_152332.2 MTL5 NM_004923.2 MTMR3 NM_021090.2 MTMR8 NM_017677.2 MUC16 NM_024690 MUC2 NM_002457 MUF1 NM_006369.3 MULK NM_018238.2 MYBPC2 NM_004533 MYCBP2 NM_015057 MYH1 NM_005963.2 MYH7B NM_020884 MYH9 NM_002473.2 MYLC2PL NM_138403 MYO15A NM_016239 MYO18B NM_032608 MYO1G NM_033054 MYO7A NM_000260 MYO9B NM_004145 MYOD1 NM_002478.3 MYR8 NM_015011 MYST4 NM_012330.1 N4BP2 NM_018177.2 NAG6 NM_022742 NALP1 NM_014922 NALP14 NM_176822.2 NALP8 NM_176811.2 NALP9 NM_176820.2 NAV3 NM_014903 NCAM1 NM_000615 NCB5OR NM_016230.2 NCOA6 NM_014071.2 NDRG2 NM_201541.1 NDST1 NM_001543 NDUFA2 NM_002488.2 NDUFA3 NM_004542.1 NDUFA8 NM_014222.2 NEB NM_004543 NEDD4 NM_198400.1 NEF3 NM_005382.1 NET1 NM_005863.2 NF1 NM_000267.1 NF2 NM_000268.2 NFASC NM_015090 NFIX NM_002501 NFKB1 NM_003998.2 NFKBIA NM_020529.1 NFKBIE NM_004556 NFYC NM_014223.2 NGLY1 NM_018297 NHS NM_198270.2 NID2 NM_007361.2 NIPBL NM_133433.2 NOD27 NM_032206.2 NOS2A NM_000625.3 NOTCH1 NM_017617 NOTCH4 NM_004557 NOX5 NM_024505 NRCAM NM_005010.2 NRK NM_198465 NRXN3 NM_004796.3 NUFIP2 NM_020772 NUP133 NM_018230.2 NUP188 NM_015354 NUP205 NM_015135 NUP214 NM_005085.2 NUP98 NM_016320.2 NXN NM_022463.3 NYD-SP21 NM_032597 OATL1 NM_002536 OBSCN NM_052843.1 OCA2 NM_000275.1 ODZ1 NM_014253.1 OR10A2 NM_001004460 OR10H4 NM_001004465 OR12D3 NM_030959.2 OR1J2 NM_054107 OR1N1 NM_012363.1 OR1S1 NM_001004458 OR2AK2 NM_001004491 OR2M4 NM_017504 OR2W3 NM_001001957 OR2W5 NM_001004698 OR4D2 NM_001004707 OR52A1 NM_012375 OR52H1 NM_001005289 OR56A1 NM_001001917 OR5H1 NM_001005338 OR5J2 NM_001005492 OR5M11 NM_001005245 OR8B12 NM_001005195 OR8D2 NM_001002918 OR8I2 NM_001003750 OR9Q2 NM_001005283 OSBP2 NM_030758 OSBPL11 NM_022776.3 OTC NM_000531.3 OTOF NM_194323.1 P15RS NM_018170.2 PADI3 NM_016233.1 PADI6 NM_207421 PANX2 NM_052839.2 PAPPA2 NM_020318 PARP1 NM_001618.2 PCDH19 NM_020766 PCDH20 NM_022843.2 PCDH8 NM_002590.2 PCDHA10 NM_031859 PCDHA11 NM_031861 PCDHA5 NM_031501 PCDHB15 NM_018935.2 PCDHGA1 NM_031993 PCDHGA3 NM_032011 PCDHGA6 NM_032086 PCDHGB1 NM_032095 PCDHGB5 NM_032099 PCM1 NM_006197 PCNT NM_006031 PDCD11 NM_014976 PDCD4 NM_014456.3 PDCD6 NM_013232.2 PDE2A NM_002599.1 PDLIM7 NM_005451.3 PDPR NM_017990 PDZD7 NM_024895 PDZK2 NM_024791.2 PDZK4 NM_032512.2 PEBP4 NM_144962 PER1 NM_002616.1 PER2 NM_022817.1 PEX14 NM_004565 PFC NM_002621.1 PFKFB4 NM_004567.2 PGBD3 NM_170753.1 PHACS NM_032592.1 PHC1 NM_004426.1 PHF19 NM_015651 PHF7 NM_016483.4 PHKB NM_000293.1 PIGN NM_176787 PIGS NM_033198.2 PIK3C2G NM_004570 PIK3CA NM_006218 PIK3R1 NM_181523.1 PIK3R4 NM_014602.1 PKD1L1 NM_138295 PKD1L2 NM_052892 PKDREJ NM_006071.1 PKHD1L1 NM_177531 PKN1 NM_213560 PLA2G4A NM_024420.1 PLB1 NM_153021 PLCB1 NM_015192.2 PLCB2 NM_004573 PLCD3 NM_133373 PLCG1 NM_002660.2 PLD2 NM_002663.2 PLEKHA8 NM_032639.2 PLEKHG2 NM_022835 PLOD1 NM_000302.2 PLS3 NM_005032.3 PLXNB1 NM_002673.3 PNCK NM_198452.1 PNLIPRP1 NM_006229.1 PNPLA1 NM_001039725 PODXL NM_001018111 POLH NM_006502.1 POLR2F NM_021974.2 POP1 NM_015029.1 POU2F1 NM_002697.2 POU4F2 NM_004575 PP NM_021129.2 PPAPDC1A NM_001030059 PPFIBP2 NM_003621 PPHLN1 NM_201439.1 PPM1E NM_014906.3 PPM1F NM_014634.2 PPP1R12A NM_002480 PPP1R3A NM_002711.2 PRDM13 NM_021620 PRDM4 NM_012406.3 PRDX5 NM_012094.3 PRKAA1 NM_006251.4 PRKAA2 NM_006252.2 PRODH NM_016335.2 PRPF39 NM_017922.2 PRPF4B NM_176800.1 PRPS1 NM_002764.2 PRPS1L1 NM_175886 PRRG1 NM_000950.1 PRSS7 NM_002772.1 PSD NM_002779 PSME4 NM_014614 PSPC1 NM_018282 PSRC2 NM_144982 PTD004 NM_013341.2 PTHLH NM_198964.1 PTPN14 NM_005401.3 PTPN6 NM_080548 PTPRC NM_002838.2 PTRF NM_012232.2 PURG NM_013357.2 PUS1 NM_025215.3 PUS7 NM_019042 RAB41 NM_001032726 RABEP2 NM_024816 RAC2 NM_002872.3 RAI17 NM_020338.1 RANBP1 NM_002882.2 RANBP3 NM_007321 RANBP3 NM_007322 RAP1GA1 NM_002885.1 RAPH1 NM_213589.1 RARG NM_000966.3 RASAL2 NM_170692.1 RASGRF2 NM_006909.1 RASL10B NM_033315.2 RBAF600 NM_020765.1 RBM25 NM_021239 RCE1 NM_005133.1 RFC4 NM_181573.1 RFX2 NM_000635.2 RG9MTD2 NM_152292.2 RGL1 NM_015149.2 RGS22 NM_015668 RHAG NM_000324.1 RHD NM_016124.2 RIF1 NM_018151.1 RIMS1 NM_014989 RIMS2 NM_014677 RLTPR NM_001013838 RNF123 NM_022064 RNF127 NM_024778.3 RNF149 NM_173647.2 RNU3IP2 NM_004704.2 ROBO3 NM_022370 ROR1 NM_005012.1 RP1L1 NM_178857 RPGRIP1 NM_020366 RPL3 NM_000967.2 RPRC1 NM_018067 RPS26 NM_001029 RPS6KA3 NM_004586.1 RPS9 NM_001013.2 RPUSD4 NM_032795.1 RREB1 NM_001003699 RSN NM_002956.2 RTP1 NM_153708.1 RTTN NM_173630 RUFY1 NM_025158.2 RYR1 NM_000540 RYR2 NM_001035 SAMD9 NM_017654 SAPS1 NM_014931 SATL1 NM_001012980 SBNO1 NM_018183.2 SCARF2 NM_153334.3 SCGB3A2 NM_054023.2 SCML1 NM_006746.2 SCN2A2 NM_021007 SCN3A NM_006922 SCNN1B NM_000336.1 SCP2 NM_002979.2 SEC31L1 NM_014933.2 SEMA3A NM_006080.1 SEMA4B NM_198925 SEMA4G NM_017893.2 SEMA5B NM_018987.1 SEMA6D NM_153616 SEMA7A NM_003612.1 SEPHS2 NM_012248 SERPINB1 NM_030666.2 SERPINB11 NM_080475 SERPINE2 NM_006216.2 SF3B1 NM_012433 SF3B2 NM_006842 SFRS1 NM_006924.3 SFRS16 NM_007056.1 SGKL NM_013257.3 SH2D3A NM_005490.1 SH3RF1 NM_020870 SHCBP1 NM_024745.2 SIGLEC5 NM_003830 SIPA1L1 NM_015556.1 SIX4 NM_017420.1 SKIP NM_016532.2 SKIV2L NM_006929.3 SLAMF1 NM_003037.1 SLC12A3 NM_000339.1 SLC16A2 NM_006517.1 SLC17A6 NM_020346.1 SLC22A2 NM_003058.2 SLC22A9 NM_080866.2 SLC25A30 NM_001010875 SLC35A2 NM_005660.1 SLC35F1 NM_001029858 SLC38A3 NM_006841 SLC39A12 NM_152725.1 SLC4A3 NM_005070.1 SLC6A3 NM_001044.2 SLC6A5 NM_004211.1 SLC7A7 NM_003982.2 SLC8A3 NM_033262.3 SLC8A3 NM_182932.1 SLC9A10 NM_183061 SLC9A2 NM_003048.3 SLCO2B1 NM_007256.2 SLFN13 NM_144682 SLICK NM_198503.2 SMARCAL1 NM_014140.2 SMC4L1 NM_005496.2 SMC6L1 NM_024624.2 SMOX NM_175839.1 SN NM_023068.2 SNTG2 NM_018968 SNX25 NM_031953 SOHLH1 NM_001012415 SORBS1 NM_015385.1 SORCS1 NM_052918.2 SORL1 NM_003105.3 SOX13 NM_005686 SOX15 NM_006942 SP110 NM_004509.2 SPAG6 NM_012443.2 SPATS2 NM_023071 SPCS2 NM_014752 SPEN NM_015001.2 SPG4 NM_014946.3 SPINK5 NM_006846 SPO11 NM_012444.2 SPOCD1 NM_144569.3 SPTA1 NM_003126 SPTAN1 NM_003127.1 SPTBN1 NM_178313 SPTLC1 NM_006415.2 SPTY2D1 NM_194285 SREBF2 NM_004599.2 SRGAP3 NM_014850.1 SSFA2 NM_006751.3 SSNA1 NM_003731.1 ST8SIA3 NM_015879 STAB1 NM_015136 STARD8 NM_014725.2 STAT1 NM_007315.2 STAT4 NM_003151.2 STATIP1 NM_018255.1 STRBP NM_018387.2 STX12 NM_177424.1 STX5A NM_003164.2 SULF2 NM_018837.2 SULT6B1 NM_001032377 SUPT3H NM_181356 SURF1 NM_003172.2 SUSD3 NM_145006.2 SUV39H2 NM_024670.3 SYNE2 NM_182914.1 SYT3 NM_032298.1 SYTL2 NM_032943 TAC4 NM_170685 TACC2 NM_206862.1 TAF1 NM_004606.2 TAF1B NM_005680 TA-KRP NM_032505.1 TAS2R13 NM_023920.1 TAX1BP1 NM_006024.4 TBC1D19 NM_018317.1 TBC1D2B NM_015079 TBX1 NM_005992.1 TBXAS1 NM_001061.2 TCEAL5 NM_001012979 TCF1 NM_000545.3 TCF7L1 NM_031283.1 TCFL1 NM_005997.1 TCP1 NM_030752.1 TCP10 NM_004610 TDRD6 NM_001010870 TECTA NM_005422.1 TEK NM_000459.1 TESK1 NM_006285.1 TESK2 NM_007170 TEX11 NM_031276 TFAP2D NM_172238.1 TG NM_003235 TGM3 NM_003245 THBS3 NM_007112.3 THG-1 NM_030935.3 TIAM2 NM_001010927 TIFA NM_052864 TIMELESS NM_003920.1 TLL1 NM_012464.3 TLN1 NM_006289 TLN2 NM_015059 TM4SF7 NM_003271.3 TMED1 NM_006858.2 TMEM123 NM_052932 TMEM132B NM_052907 TMEM28 NM_015686 TMEM37 NM_183240 TMEM39A NM_018266.1 TMEM62 NM_024956 TMEM63A NM_014698 TMPRSS3 NM_024022.1 TMPRSS6 NM_153609.1 TNFRSF25 NM_003790.2 TNS NM_022648.2 TOP1 NM_003286.2 TOP2B NM_001068 TP53 NM_000546.2 TPM4 NM_003290.1 TPTE NM_199261.1 TRAD NM_007064.1 TREM1 NM_018643.2 TREML1 NM_178174.2 TREML4 NM_198153 TRIAD3 NM_207116 TRIF NM_182919.1 TRIM25 NM_005082.3 TRIM29 NM_012101.2 TRIM36 NM_018700.2 TRIOBP NM_001039141 TRIP12 NM_004238 TRPC4 NM_016179.1 TRPM5 NM_014555 TSN NM_004622 TTC15 NM_016030.5 TTC21B NM_024753 TTC3 NM_003316.2 TTC7A NM_020458 TTN NM_133378 TXNDC3 NM_016616.2 UBE2I NM_194261.1 UBE2O NM_022066 UGT1A9 NM_021027.2 UNQ9356 NM_207410.1 UQCR NM_006830.2 USP29 NM_020903 USP34 NM_014709 USP54 NM_152586.2 UTP14C NM_021645 UTS2R NM_018949.1 VAV3 NM_006113.3 VEPH1 NM_024621.1 VGCNL1 NM_052867.1 VWF NM_000552.2 WARS NM_173701.1 WBP4 NM_007187.3 WBSCR28 NM_182504 WDR48 NM_020839 WDR53 NM_182627.1 WDR60 NM_018051 WDSOF1 NM_015420 WFDC1 NM_021197.2 WNK1 NM_018979.1 WNT2 NM_003391.1 XAB2 NM_020196 XBP1 NM_005080.2 XDH NM_000379.2 XKR7 NM_001011718 XPO5 NM_020750 XPO7 NM_015024 YY2 NM_206923.1 ZBTB3 NM_024784.2 ZBTB39 NM_014830 ZCCHC14 NM_015144.1 ZCSL3 NM_181706.3 ZDHHC4 NM_018106.2 ZFHX4 NM_024721 ZFP64 NM_199427.1 ZFYVE26 NM_015346.2 ZIC3 NM_003413.2 ZNF10 NM_015394.4 ZNF124 NM_003431 ZNF532 NM_018181.3 ZNF541 NM_032255.1 ZNF546 NM_178544.2 ZNF548 NM_152909 ZNF569 NM_152484.2 ZNF644 NM_201269.1 ZNF646 NM_014699.2 ZNF142 NM_005081 ZNF161 NM_007146 ZNF183 NM_006978.1 ZNF22 NM_006963.2 ZNF25 NM_145011.2 ZNF267 NM_003414 ZNF277 NM_021994.1 ZNF281 NM_012482.3 ZNF674 NM_001039891 ZNF694 NM_001012981 ZNF707 NM_173831 ZNF75A NM_153028.1 ZNHIT2 NM_014205.2 ZNF318 NM_014345.1 ZNF37A NM_001007094 ZNF425 NM_001001661 ZNF432 NM_014650.2 ZNF436 NM_030634.1 ZNF529 NM_020951 Note: Gene symbols are standard symbols assigned by Entrz Gene (http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene). Accession IDs “NM_XXXX” are uniquely assigned to each gene by National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/sites/entrez?db=nuccore)

TABLE 15 Genes containing somatic mutations in colorectal cancer adapted from the paper by Wood et. al.(Wood et al., 2007). Gene Symbol Accession ID ABCA1 NM_005502.2 ABCA6 NM_080284.2 ABCB1 NM_000927.3 ABCB11 NM_003742 ABCB5 NM_178559.3 ABCC5 NM_005688 ABCD4 NM_005050.1 ABI3BP NM_015429 ACACA NM_198839.1 ACIN1 NM_014977.1 ACSL4 NM_022977.1 ACSL5 NM_016234.3 AD026 NM_020683.5 ADAM19 NM_033274.1 ADAM29 NM_014269.2 ADAM33 NM_025220.2 ADAM8 NM_001109 ADAMTS1 NM_006988 ADAMTS15 NM_139055.1 ADAMTS18 NM_199355.1 ADAMTS20 NM_025003 ADAMTS20 NM_175851 ADAMTSL3 NM_207517.1 ADARB2 NM_018702.1 ADCY8 NM_001115.1 ADCY9 NM_001116 ADD3 NM_016824.2 ADORA1 NM_000674.1 AFMID NM_001010982 AGTPBP1 NM_015239.1 AIM1 NM_001624 AKAP12 NM_005100.2 AKAP3 NM_006422.2 AKAP6 NM_004274.3 AKAP9 NM_005751.3 ALDH1L1 NM_012190.2 ALG9 NM_024740 ALK NM_004304 ALS2CR11 NM_152525.3 ALS2CR8 NM_024744 AMACO NM_198496.1 AMOTL2 NM_016201 AMPD1 NM_000036.1 AMPD3 NM_000480.1 ANAPC4 NM_013367.2 ANK2 NM_001148.2 ANKFN1 NM_153228 ANKRD11 NM_013275 ANKRD26 NM_014915 APBB2 NM_173075 APC NM_000038.2 APG5L NM_004849.1 API5 NM_006595 APIN NM_017855.2 APOB NM_000384.1 APOB48R NM_182804 AQR NM_014691 ARAF NM_001654 ARFGEF1 NM_006421.2 ARHGEF1 NM_199002.1 ARHGEF10 NM_014629 ARHGEF9 NM_015185 ARR3 NM_004312.1 ASCC3L1 NM_014014.2 ASE-1 NM_012099.1 ATAD1 NM_032810.2 ATP11A NM_032189 ATP11C NM_173694.2 ATP12A NM_001676 ATP13A1 NM_020410 ATP13A5 NM_198505 ATP13A5 NM_198505 ATP6V1E1 NM_001696.2 ATP8A2 NM_016529 ATP8B4 NM_024837 AVPR1B NM_000707 AZI1 NM_001009811 BCAP29 NM_001008405 BCAS2 NM_005872.1 BCL11B NM_022898.1 BCL9 NM_004326 BICD1 NM_001714.1 BMP6 NM_001718.2 BMPR2 NM_001204 BPIL1 NM_025227.1 BRAF NM_004333.2 BRF1 NM_001519.2 BRUNOL6 NM_052840.2 BTBD4 NM_025224.1 BTF3L4 NM_152265 C10orf137 NM_015608.2 C10orf28 NM_014472 C10orf64 NM_173524 C10orf72 NM_144984.1 C12orf11 NM_018164.1 C13orf7 NM_024546 C14orf115 NM_018228.1 C15orf2 NM_018958.1 C17orf27 NM_020914 C17orf46 NM_152343 C17orf49 NM_174893 C18orf4 NM_032160.1 C1QR1 NM_012072.2 C20orf23 NM_024704.3 C21orf18 NM_017438.1 C21orf29 NM_144991.2 C21orf88 NM_153754 C2orf10 NM_194250.1 C2orf16 NM_032266 C2orf33 NM_020194.4 C4BPA NM_000715.2 C4orf15 NM_024511 C6orf191 NM_001010876 C6orf29 NM_025257.1 C8B NM_000066 C9orf21 NM_153698 Cab45 NM_016547.1 CACNA1A NM_000068 CACNA1B NM_000718 CACNA2D3 NM_018398 CACNB1 NM_199247.1 CACNB2 NM_201596.1 CAD NM_004341.3 CAPN10 NM_023086.1 CAPN13 NM_144575 CAPN6 NM_014289.2 CARD12 NM_021209 CBFA2T3 NM_005187.4 CCAR1 NM_018237.2 CCNB3 NM_033031.1 CD109 NM_133493.1 CD248 NM_020404.2 CD99L2 NM_134445.1 CDC14A NM_003672.2 CDH13 NM_001257 CDH18 NM_004934.2 CDH23 NM_022124 CDH6 NM_004932.2 CDKL5 NM_003159.1 CDO1 NM_001801.1 CDS1 NM_001263.2 CEACAM20 NM_198444 CENPF NM_016343 CENPH NM_022909.3 CENTB1 NM_014716.2 CENTB2 NM_012287 CENTD3 NM_022481.4 CGI-14 NM_015944.2 CHD7 NM_017780 CHD8 NM_020920 CHL1 NM_006614.2 CHR415SYT NM_001014372 CHST8 NM_022467.3 CINP NM_032630.2 CIR NM_004882.3 CLIC2 NM_001289.3 CLSTN2 NM_022131.1 CLSTN3 NM_014718.2 CMKOR1 NM_020311.1 CNKSR2 NM_014927.2 CNOT6L NM_144571 CNTN1 NM_001843.2 CNTN4 NM_175613.1 COL12A1 NM_004370 COL3A1 NM_000090.2 COL4A6 NM_001847.1 CORO1B NM_020441.1 CORO2B NM_006091.1 CPAMD8 NM_015692 CPE NM_001873.1 CPO NM_173077.1 CRB1 NM_201253.1 CRNKL1 NM_016652 CSDA NM_003651.3 CSE1L NM_001316.2 CSMD1 NM_033225 CSMD3 NM_198123.1 CSNK1A1L NM_145203.2 CTCFL NM_080618.2 CTEN NM_032865.3 CTNNA1 NM_001903 CTNND2 NM_001332.2 CTSH NM_004390.2 CUBN NM_001081.2 CUTL1 NM_001913.2 CX40.1 NM_153368.1 CXorf53 NM_024332 CYP4F8 NM_007253 DACT1 NM_016651.4 DBC1 NM_014618.1 DCC NM_005215.1 DCHS1 NM_003737.1 DDEFL1 NM_017707.2 DDHD2 NM_015214 DDI1 NM_001001711 DDIT3 NM_004083.3 DDN NM_015086 DDX53 NM_182699 DEFA4 NM_001925.1 DEFB111 NM_001037497 DENND1C NM_024898 DEPDC2 NM_024870.2 DGCR2 NM_005137 DHRS2 NM_005794.2 DJ167A19.1 NM_018982.3 DKFZp761I2123 NM_031449 DLG3 NM_021120.1 DMD NM_004021.1 DMD NM_004006.1 DMRTA1 NM_022160.1 DNAH1 NM_015512 DNAH11 NM_003777 DNAH3 NM_017539.1 DNAH8 NM_001371.1 DNAJC10 NM_018981 DNAJC6 NM_014787 DNALI1 NM_003462.3 DNAPTP6 NM_015535 DNASE1L3 NM_004944.1 DPEP1 NM_004413.1 DPP10 NM_020868 DPYSL2 NM_001386.3 DSCAML1 NM_020693.2 DSTN NM_006870.2 DTNB NM_183361 DUSP21 NM_022076.2 DUX4C NM_001023569 EDA NM_001399.3 EDD1 NM_015902 EFS NM_005864.2 EIF2S2 NM_003908.2 EIF4G1 NM_198241.1 EML1 NM_004434 EML2 NM_012155.1 EN1 NM_001426.2 ENPP2 NM_006209.2 EPHA3 NM_005233.3 EPHA4 NM_004438.3 EPHA7 NM_004440.2 EPHB1 NM_004441 EPHB6 NM_004445.1 ERCC6 NM_000124.1 ESSPL NM_183375 ETAA16 NM_019002.2 ETFDH NM_004453.1 EVC2 NM_147127.2 EVL NM_016337.1 EYA4 NM_004100.2 EZH2 NM_004456.3 F5 NM_000130.2 F8 NM_000132 FAM102B NM_001010883 FAM19A5 NM_015381 FAM26A NM_182494 FAM3A NM_021806 FAM40A NM_033088 FANCG NM_004629.1 FAT NM_005245 FBN1 NM_000138 FBN2 NM_001999 FBXL2 NM_012157.2 FBXO30 NM_032145.3 FBXW7 NM_033632.1 FCN1 NM_002003.2 FCN2 NM_004108.1 FERD3L NM_152898.2 FGF13 NM_033642.1 FGF14 NM_175929.1 FHOD3 NM_025135 FIGN NM_018086.1 FLJ10241 NM_018035 FLJ10404 NM_019057 FLJ10490 NM_018111 FLJ10521 NM_018125.2 FLJ10560 NM_018138.1 FLJ10665 NM_018173.1 FLJ10996 NM_019044.2 FLJ11000 NM_018295.1 FLJ12770 NM_032174.3 FLJ13305 NM_032180 FLJ14803 NM_032842 FLJ16171 NM_001004348 FLJ16542 NM_001004301 FLJ20294 NM_017749 FLJ20729 NM_017953.2 FLJ21019 NM_024927.3 FLJ21986 NM_024913 FLJ22679 NM_032227.1 FLJ25477 NM_199138.1 FLJ32252 NM_182510 FLJ32312 NM_144709.1 FLJ33534 NM_182586.1 FLJ34633 NM_152365.1 FLJ34922 NM_152270.2 FLJ35834 NM_178827.3 FLJ36119 NM_153254.1 FLJ38964 NM_173527 FLJ40142 NM_207435.1 FLJ42418 NM_001001695 FLJ43339 NM_207380.1 FLJ43980 NM_001004299 FLJ44653 NM_001001678 FLJ45273 NM_198461.1 FLJ46082 NM_207417.1 FLJ46154 NM_198462.1 FLNC NM_001458 FMN2 NM_020066 FN1 NM_002026.2 FNDC1 NM_032532 FOLH1 NM_004476.1 FRAS1 NM_025074 FRAS1 NM_032863 FRMPD2 NM_152428.2 FRMPD4 NM_014728 FRY NM_023037 FSTL5 NM_020116.2 FZD4 NM_012193.2 GAB4 NM_001037814 GABPB2 NM_016654.2 GABRA6 NM_000811.1 GALGT2 NM_153446.1 GALNS NM_000512.2 GDAP1L1 NM_024034.3 GFI1 NM_005263 GFI1B NM_004188.2 GHRHR NM_000823.1 GJA8 NM_005267 GLB1 NM_000404 GLI3 NM_000168.2 GLIPR1 NM_006851.1 GMCL1L NM_022471.2 GNAS NM_000516.3 GNRH1 NM_000825 GPBP1 NM_022913 GPR112 NM_153834 GPR124 NM_032777.6 GPR158 NM_020752 GPR50 NM_004224 GPR8 NM_005286.2 GPR87 NM_023915.2 GPX1 NM_000581 GRID1 NM_017551 GRID2 NM_001510.1 GRIK1 NM_175611 GRIK3 NM_000831.2 GRM1 NM_000838.2 GTF2B NM_001514.2 GUCY1A2 NM_000855.1 HAPIP NM_003947.1 HAPLN1 NM_001884.2 HAT1 NM_003642.1 HBXIP NM_006402.2 HCAP-G NM_022346.2 HDC NM_002112.1 HECTD1 NM_015382 HIC1 NM_006497 HIST1H1B NM_005322.2 HIST1H1E NM_005321.2 HIST1H2BM NM_003521.2 HIVEP1 NM_002114 HIVEP3 NM_024503.1 HK3 NM_002115.1 HOXC9 NM_006897.1 HPS3 NM_032383.3 HR NM_005144.2 HRH1 NM_000861.2 HS3ST4 NM_006040 HSPG2 NM_005529 HTR3C NM_130770.2 HTR5A NM_024012.1 HUWE1 NM_031407 IDH1 NM_005896.2 IGFBP3 NM_000598.2 IGSF22 NM_173588 IGSF9 NM_020789.2 IK NM_006083 IL6ST NM_002184.2 IQSEC3 NM_015232 IREM2 NM_181449.1 IRS2 NM_003749.2 IRS4 NM_003604.1 ISLR NM_201526.1 ITGAE NM_002208 ITGB3 NM_000212.2 ITPR1 NM_002222 K6IRS3 NM_175068.2 KCNA10 NM_005549.2 KCNB2 NM_004770.2 KCNC4 NM_004978.2 KCND3 NM_004980.3 KCNH4 NM_012285.1 KCNQ5 NM_019842.2 KCNT1 NM_020822 KCTD16 NM_020768 KDR NM_002253.1 KIAA0182 NM_014615.1 KIAA0367 NM_015225 KIAA0415 NM_014855 KIAA0528 NM_014802 KIAA0555 NM_014790.3 KIAA0556 NM_015202 KIAA0789 NM_014653 KIAA0934 NM_014974.1 KIAA1078 NM_203459.1 KIAA1185 NM_020710.1 KIAA1285 NM_015694 KIAA1409 NM_020818.1 KIAA1468 NM_020854.2 KIAA1529 NM_020893 KIAA1727 NM_033393 KIAA1875 NM_032529 KIAA2022 NM_001008537 KIF13A NM_022113 KL NM_004795.2 KLF5 NM_001730.2 KLRF1 NM_016523 KRAS NM_004985.3 KRT20 NM_019010.1 KRTAP10-2 NM_198693 KRTAP10-8 NM_198695.1 KSR2 NM_173598 LAMA1 NM_005559 LAMA4 NM_002290 LAMB3 NM_000228.1 LAMB4 NM_007356 LAMC1 NM_002293.2 LAS1L NM_031206.2 LCN10 NM_001001712 LCN9 NM_001001676 LDB1 NM_003893.3 LDLRAD1 NM_001010978 LEF1 NM_016269.2 LGR6 NM_021636.1 LIFR NM_002310.2 LIG1 NM_000234.1 LIG3 NM_013975.1 LILRB1 NM_006669 LMNB2 NM_032737.2 LMO7 NM_005358.3 LOC122258 NM_145248.2 LOC126147 NM_145807 LOC129531 NM_138798.1 LOC157697 NM_207332.1 LOC167127 NM_174914.2 LOC223075 NM_194300.1 LOC388199 NM_001013638 LOC91807 NM_182493.1 LPIN1 NM_145693.1 LPPR2 NM_022737.1 LRCH4 NM_002319 LRP1 NM_002332.1 LRP2 NM_004525.1 LRRC4 NM_022143.3 LRRN6D NM_001004432 LRTM2 NM_001039029 LSP1 NM_001013253 LZTS2 NM_032429.1 MAMDC1 NM_182830 MAN2A2 NM_006122 MAP1B NM_005909.2 MAP2 NM_002374.2 MAP2K7 NM_145185 MAPK8IP2 NM_012324 MARLIN1 NM_144720.2 MAST1 NM_014975 MCF2L2 NM_015078.2 MCM3AP NM_003906.3 MCP NM_172350.1 MCRS1 NM_006337.3 MED12L NM_053002 MEF2C NM_002397 MEGF6 NM_001409 MET NM_000245 MFN1 NM_033540.2 MGC13125 NM_032725.2 MGC15730 NM_032880.2 MGC16943 NM_080663.1 MGC20470 NM_145053 MGC26733 NM_144992 MGC29671 NM_182538.3 MGC32124 NM_144611.2 MGC33407 NM_178525.2 MGC33846 NM_175885 MGC39325 NM_147189.1 MGC39545 NM_203452.1 MGC48628 NM_207491 MGC52022 NM_198563.1 MGC52282 NM_178453.2 MGC5242 NM_024033.1 MGC8685 NM_178012.3 MKRN3 NM_005664.1 MLF2 NM_005439.1 MLL3 NM_170606.1 MMP11 NM_005940.2 MMP2 NM_004530.1 MMRN2 NM_024756.1 MN1 NM_002430 MPO NM_000250.1 MPP3 NM_001932 MRGPRE NM_001039165 MRPL23 NM_021134 MS4A5 NM_023945.2 MTHFD1L NM_015440.3 MUC1 NM_002456.3 MUC16 NM_024690 MYADML NM_207329.1 MYO18B NM_032608 MYO1B NM_012223.2 MYO1D NM_015194 MYO5C NM_018728 MYOHD1 NM_001033579 MYR8 NM_015011 NALP7 NM_139176.2 NALP8 NM_176811.2 NAV3 NM_014903 NBEA NM_015678 NCDN NM_014284.1 NCR1 NM_004829.3 NDST3 NM_004784.1 NDUFA1 NM_004541.2 NEB NM_004543 NELL1 NM_006157.2 NEUGRIN NM_016645.1 NF1 NM_000267.1 NFATC1 NM_006162.3 NID NM_002508.1 NLGN4X NM_181332.1 NODAL NM_018055.3 NOS3 NM_000603.2 NR3C2 NM_000901.1 NTNG1 NM_014917 NUP210 NM_024923 NUP210L NM_207308 OBSCN NM_052843.1 ODZ1 NM_014253.1 OLFM2 NM_058164.1 OMA1 NM_145243.2 OR10G3 NM_001005465 OR13F1 NM_001004485 OR1E2 NM_003554.1 OR2T33 NM_001004695 OR2T34 NM_001001821 OR4A16 NM_001005274 OR4K14 NM_001004712 OR51E1 NM_152430 OR51T1 NM_001004759 OR5H6 NM_001005479 OR5J2 NM_001005492 OR5K1 NM_001004736 OR6C1 NM_001005182 OR6C6 NM_001005493 OR6C75 NM_001005497 OR8K3 NM_001005202 OSBP NM_002556.2 OSBPL5 NM_020896 OSBPL5 NM_145638 OTOP2 NM_178160.1 OVCH1 NM_183378 OVGP1 NM_002557.2 OXCT1 NM_000436.2 P2RX7 NM_002562.4 P2RY14 NM_014879.2 PAK6 NM_020168.3 PANK4 NM_018216.1 PAOX NM_207128.1 PARP8 NM_024615.2 PBEF1 NM_005746.1 PBX4 NM_025245.1 PBXIP1 NM_020524.2 PCDH11X NM_032968.2 PCDHA9 NM_014005 PCDHGA7 NM_032087 PCDHGB4 NM_032098 PCP4 NM_006198 PCSK2 NM_002594.2 PDE11A NM_016953 PDGFD NM_033135.2 PDILT NM_174924.1 PDZD2 NM_178140 PDZRN3 NM_015009 PDZRN4 NM_013377.2 PEBP4 NM_144962 PEG3 NM_006210.1 PER1 NM_002616.1 PERQ1 NM_022574 PEX5L NM_016559.1 PF6 NM_206996.1 PHIP NM_017934.4 PHKB NM_000293.1 PIGO NM_032634.2 PIK3CA NM_006218 PIK3R5 NM_014308.1 PKHD1 NM_138694.2 PKHD1L1 NM_177531 PKNOX1 NM_004571.3 PLA2G4B NM_005090 PLA2G4D NM_178034 PLB1 NM_153021 PLCG2 NM_002661 PLEC1 NM_201378 PLXND1 NM_015103 PNLIPRP2 NM_005396 PNMA3 NM_013364 PNPLA1 NM_001039725 PPM1F NM_014634.2 PPP1R12A NM_002480 PQBP1 NM_005710.1 PQLC1 NM_025078.3 PRDM9 NM_020227 PRF1 NM_005041.3 PRG2 NM_002728.4 PRIMA1 NM_178013.1 PRKCE NM_005400.2 PRKCZ NM_002744.2 PRKD1 NM_002742.1 PRKDC NM_006904 PRNPIP NM_024066 PRO0149 NM_014117.2 PROL1 NM_021225 PROS1 NM_000313.1 PRPS1 NM_002764.2 PRSS1 NM_002769.2 PRTG NM_173814 PSMA2 NM_002787.3 PSMC5 NM_002805.4 PTEN NM_000314 PTPRD NM_130391.1 PTPRH NM_002842 PTPRN2 NM_002847.2 PTPRS NM_130853.1 PTPRU NM_005704.2 PTPRZ1 NM_002851 PZP NM_002864.1 QKI NM_006775.1 RAB38 NM_022337.1 RAB5C NM_201434.1 RABEP1 NM_004703 RALGDS NM_006266.2 RAPGEF4 NM_007023 RARB NM_000965.2 RASAL2 NM_170692.1 RASGRF2 NM_006909.1 RASGRP1 NM_005739 RASSF2 NM_170774.1 RASSF4 NM_032023.3 RAVER2 NM_018211 RB1CC1 NM_014781 RBM10 NM_005676.3 RBP3 NM_002900.1 RCN1 NM_002901.1 RDH13 NM_138412 RELN NM_005045 RET NM_020975.2 REV3L NM_002912.1 RFC4 NM_181573.1 RHEB NM_005614.2 RHPN1 NM_052924 RIC3 NM_024557.2 RIMBP2 NM_015347 RIMS2 NM_014677 RNF182 NM_152737.1 RNF31 NM_017999 RNPEPL1 NM_018226.2 ROBO1 NM_002941 ROBO2 NM_002942 RORA NM_002943.2 RPA3 NM_002947.2 RPAP1 NM_015540.2 RPL6 NM_000970.2 RPS6KB1 NM_003161.1 RREB1 NM_001003699 RTN4 NM_207521.1 RUNX1T1 NM_175634.1 RYR2 NM_001035 SACS NM_014363.3 SALL2 NM_005407 SALL3 NM_171999.1 SCN10A NM_006514 SCN1A NM_006920 SCN3B NM_018400.2 SCN7A NM_002976 SCNN1B NM_000336.1 SCNN1G NM_001039.2 SDBCAG84 NM_015966.2 SDCBP2 NM_080489.2 SDK1 NM_152744 SEC24B NM_006323 SEC8L1 NM_021807.2 SEMA3D NM_152754 SERPINA3 NM_001085 SETBP1 NM_015559.1 SEZ6 NM_178860 SF3A1 NM_005877.3 SFMBT2 NM_001029880 SFRS6 NM_006275.4 SGEF NM_015595 SH3TC1 NM_018986.2 SHANK1 NM_016148.1 SHQ1 NM_018130 SIGLEC7 NM_014385.1 SKIP NM_030623 SKIV2L NM_006929.3 SLB NM_015662.1 SLC11A2 NM_000617.1 SLC12A5 NM_020708.3 SLC12A7 NM_006598 SLC1A7 NM_006671.3 SLC22A15 NM_018420 SLC22A9 NM_080866.2 SLC26A10 NM_133489.1 SLC29A1 NM_004955.1 SLC33A1 NM_004733.2 SLC37A4 NM_001467 SLC39A7 NM_006979 SLC4A9 NM_031467 SLCO1A2 NM_134431.1 SLCO1B3 NM_019844.1 SLITRK4 NM_173078.2 SLITRK6 NM_032229 SMAD2 NM_005901.2 SMAD3 NM_005902.2 SMAD4 NM_005359.3 SMTN NM_006932.3 SNRPB2 NM_198220.1 SNTG2 NM_018968 SNX5 NM_152227.1 SNX8 NM_013321.1 SOCS6 NM_004232.2 SORL1 NM_003105.3 SPOCK3 NM_016950 SPTBN2 NM_006946.1 ST8SIA4 NM_005668.3 STAB1 NM_015136 STAM NM_003473.2 STK32C NM_173575.2 STMN4 NM_030795.2 STX17 NM_017919.1 SUHW4 NM_001002843 SYNE1 NM_182961.1 SYNPO NM_007286.3 SYT9 NM_175733.2 SYTL2 NM_206927 T3JAM NM_025228.1 TAF1L NM_153809 TAF2 NM_003184 TAIP-2 NM_024969.2 TA-KRP NM_032505.1 TBC1D2B NM_015079 TBX1 NM_005992.1 TBX15 NM_152380 TBX22 NM_016954.2 TCEB3B NM_016427.2 TCERG1L NM_174937.1 TCF3 NM_003200.1 TCF7L2 NM_030756.1 TCFL5 NM_006602.2 TCOF1 NM_000356.1 TFEC NM_012252.1 TFG NM_006070.3 TGFBR2 NM_003242.3 TGM2 NM_004613.2 TGM3 NM_003245 THAP9 NM_024672.2 THRAP1 NM_005121 TIAM1 NM_003253.1 TLR8 NM_138636.2 TLR9 NM_017442.2 TM7SF4 NM_030788.2 TMEM132B NM_052907 TMEM16B NM_020373 TMPRSS4 NM_019894 TNFRSF9 NM_001561.4 TNN NM_022093 TNNI3K NM_015978.1 TOP2A NM_001067 TP53 NM_000546.2 TP53BP1 NM_005657.1 TPX2 NM_012112.4 TREX2 NM_080701 TRIM3 NM_033278.2 TRIM71 NM_001039111 TRMT5 NM_020810 TSKS NM_021733.1 TSN NM_004622 TSP-NY NM_032573.3 TSPYL5 NM_033512 TTID NM_006790.1 TTLL3 NM_015644.1 TTN NM_133378 TTYH2 NM_032646 TXLNB NM_153235 TYSND1 NM_173555 UBE3C NM_014671 UGDH NM_003359.1 UHRF2 NM_152896.1 UNC13B NM_006377.2 UNC84B NM_015374.1 UNQ689 NM_212557.1 UQCRC2 NM_003366.1 USP28 NM_020886 USP32 NM_032582 USP52 NM_014871.2 UTP14C NM_021645 UTX NM_021140.1 VEST1 NM_052958.1 VIM NM_003380.1 VPS13A NM_033305.1 WAC NM_016628.2 WDR19 NM_025132 WDR49 NM_178824.3 WNK1 NM_018979.1 WNT16 NM_016087.2 WNT8B NM_003393.2 WRN NM_000553.2 XKR3 NM_175878 XPO4 NM_022459 XRCC1 NM_006297.1 YEATS2 NM_018023 ZAN NM_173059 ZBTB8 NM_144621.2 ZD52F10 NM_033317.2 ZDHHC7 NM_017740.1 ZFHX1B NM_014795.2 ZFHX4 NM_024721 ZFPM2 NM_012082 ZNF155 NM_198089.1 ZNF217 NM_006526.2 ZNF232 NM_014519.2 ZNF235 NM_004234 ZNF262 NM_005095.2 ZNF291 NM_020843 ZNF43 NM_003423.1 ZNF435 NM_025231.1 ZNF442 NM_030824.1 ZNF471 NM_020813.1 ZNF480 NM_144684.1 ZNF521 NM_015461 ZNF536 NM_014717 ZNF540 NM_152606.2 ZNF560 NM_152476.1 ZNF568 NM_198539 ZNF572 NM_152412.1 ZNF582 NM_144690 ZNF624 NM_020787.1 ZNF659 NM_024697.1 ZNF714 NM_182515 ZNHIT1 NM_006349.2 ZNRF4 NM_181710 ZSCAN5 NM_024303.1 ZZZ3 NM_015534.3 Note: Gene symbols are standard symbols assigned by Entrz Gene (http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene). Accession IDs “NM_XXXX” are uniquely assigned to each gene by National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/sites/entrez?db=nuccore). 

1. A method for aiding in the diagnosis, prognosis, monitoring of disease progression, analysis of disease recurrence, and/or monitoring treatment effectiveness of a disease or other medical condition in a subject, the method comprising the steps of detecting nucleic acids within a microvesicle fraction of a biological sample from the subject, and analyzing the nucleic acids within the microvesicle fraction for the presence or absence of a biomarker.
 2. The method of claim 1, wherein the disease or other medical condition is a disease or medical condition associated with immune response, immunotherapy, cell migration, angiogenesis, cell proliferation, histone modification, organ transplantation, neurodegenerative disease, cancer, or combinations thereof.
 3. The method of claim 1, wherein the biomarker is: (i) a species of nucleic acid; (ii) the level of expression of a nucleic acid; (iii) a nucleic acid variant; (iv) a genetic aberration; or (v) a combination thereof.
 4. The method of claim 1, wherein the biomarker is messenger RNA, microRNA, siRNA, shRNA, noncoding RNA, DNA, single stranded DNA, complementary DNA, noncoding DNA, mitochondrial DNA, mitochondrial RNA, viral nucleic acid, or combinations thereof.
 5. The method of claim 1, wherein the biomarker is associated with prostate cancer, wherein the biomarker is selected from the group consisting of one or more of HOXA6, HOXC10, HOXC9, HOXD4, HOXA3, HOXA4, HOXC6, DLX1, and HK3(KLK3).
 6. The method of claim 1, wherein the biomarker is associated with immune response, wherein the biomarker is selected from the group consisting of one or more of IFN-alpha, ICAM, VEGF, CD86, IL-6, IL-8, CXL2, HLA-E, TGFBR2, HLA-F, HLA-DRA, and TNFAIP6.
 7. The method of claim 1, wherein the biomarker is an indicator of one or more chromosomal aberrations selected from the group consisting of trisomy 21, trisomy 18, trisomy 13, trisomy 16, trisomy 22, triploidy, and sex chromosome or other aneuploidy.
 8. The method of claim 1, wherein the biomarker is a marker of somatic mutation, wherein the biomarker is selected from the group consisting of one or more of BRAF, KRAS, EGFRvIII, RB, PTEN, p16, p21 and p53, and EGFR.
 9. A method for aiding in the diagnosis, prognosis, screening, monitoring, disease progression or other medical condition in a subject the method comprising the steps of detecting protein in a microvesicle fraction of a biological sample from the subject, and analyzing the proteins for the presence or absence of a biomarker.
 10. The method of claim 9, wherein the disease or other medical condition is a disease or medical condition associated with immune response, immunotherapy, cell migration, angiogenesis, cell proliferation, histone modification, organ transplantation, neurodegenerative disease, cancer, or combinations thereof.
 11. The method in claim 9, wherein the biomarker is: (i) one or more species of protein; (ii) the level of abundance of one or more proteins; (iii) one or more protein variants; (iv) a protein modification; or (iv) a combination thereof.
 12. The method of claim 11, wherein the protein modification is a post translational modification.
 13. The method of claim 11, wherein the protein modification comprises at least phosphorylation, ubiquitination, or a combination thereof.
 14. The method of claim 9, wherein the biomarker is associated with immune response and/or neurodegenerative disease, wherein the biomarker is selected from the group consisting of one or more of checkpoint inhibitors, PD1, PDL1, Tau, phospho-Tau, amyloid beta, and alpha synuclein.
 15. A method for isolating a microvesicle fraction from a biological sample, comprising the step of isolating the microvesicle fraction comprises pre-processing the biological sample to exclude proteins, lipids, debris from dead cells, and other contaminants.
 16. The method of claim 15, wherein the isolation of the microvesicle fraction is performed by size exclusion chromatography, density gradient centrifugation, differential centrifugation, nanomembrane ultrafiltration, immunoabsorbent capture, affinity purification, charge-based affinity purification, microfluidic separation, or combinations thereof.
 17. The method of claim 16, wherein the pre-processing is performed by filtering through a 0.8 μm filter, or by a combination of filtering through a 0.8 μm filter followed by size exclusion chromatography, density gradient centrifugation, differential centrifugation, nanomembrane ultrafiltration, immunoabsorbent capture, affinity purification, charge-based affinity purification, microfluidic separation, or combinations thereof.
 18. The method of claim 1, wherein the microvesicle fraction is purified prior to analysis.
 19. The method of claim 18, wherein the microvesicle fraction is concentrated, enriched, or depleted prior to nucleic acid analysis or prior to protein analysis.
 20. The method of claim 18, wherein the microvesicle fraction is purified using ultracentrifugation or a nanomembrane ultrafiltration concentrator.
 21. The method of claim 1, wherein the nucleic acid analysis is performed by microarray analysis, a PCR-based analysis, hybridization with allele-specific probes, enzymatic mutation detection, ligation chain reaction (LCR), oligonucleotide ligation assay (OLA), flow-cytometric heteroduplex analysis, chemical cleavage of mismatches, mass spectrometry, ribonucleic acid (RNA) sequencing, DNA sequencing, or a combined RNA/DNA sequencing, single strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), restriction fragment polymorphisms, serial analysis of gene expression (SAGE), DNA sequencing, or combinations thereof.
 22. The method of claim 21, wherein the PCR-based analysis is selected from the group consisting of polymerase chain reaction (PCR), in situ polymerase chain reaction, quantitative polymerase chain reaction, nested polymerase chain reaction, self-sustained sequence replication, transcriptional amplification system, Qb Replicase, cold-PCR, nested-PCR, and combinations thereof.
 23. The method of claim 1, wherein the nucleic acids are extracted from the microvesicle fraction prior to analysis.
 24. The method of claim 1, wherein the biological sample comprises blood, plasma, serum, urine, sputum, spinal fluid, pleural fluid, nipple aspirates, lymph fluid, fluid of the respiratory, intestinal, and genitourinary tracts, tear fluid, saliva, breast milk, fluid from the lymphatic system, semen, cerebrospinal fluid, intra-organ system fluid, ascitic fluid, tumor cyst fluid, amniotic fluid, or combinations thereof.
 25. A method for enriching or excluding a specific portion of a microvesicle fraction comprising a specific cell type, a specific origin, one or more distinct cell-surface proteins, one or more distinct cell-surface glycoproteins, one or more distinct cell-surface lipoproteins, one or more distinct cell-surface lipids, one or more distinct cell-surface sugars, or combinations thereof.
 26. The method of claim 25 further comprising detecting nucleic acids or proteins within a microvesicle fraction of a biological sample from the subject, and analyzing the nucleic acids or proteins within a microvesicle fraction for the presence or absence of a biomarker for use in the diagnosis, prognosis, screening, monitoring of disease progression, analysis of disease recurrence, monitoring treatment effectiveness, or combinations thereof of a disease or other medical condition in the subject.
 27. A method for aiding in the diagnosis, prognosis, screening, monitoring disease progression, evaluation, analysis of disease recurrence, monitoring treatment effectiveness of, or combinations thereof, the method comprising detecting nucleic acids or proteins within a microvesicle fraction of a biological sample from the subject, wherein the disease or other medical condition is related to the immune response against cancer.
 28. A method for analyzing nucleic acids comprising analyzing nucleic acids extracted from a microvesicle fraction in a subject to create a microvesicle biomarker profile, comparing the microvesicle biomarker profile to a control profile, and selecting one or more biomarkers based on one or more differences between the microvesicle profile and the control profile.
 29. A method for detection or analysis of messenger RNA or other long RNA extracted from a microvesicle fraction in a subject. 